rs104886471

Variant names:

• chr7-151186460-G-A
• rs104886471
• NM_001142459.2:c.516C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-151186460-G-A
• chr7-151186460-G-C

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The ENST00000420175.3(ASB10):​c.516C>T​(p.Ala172Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000166 in 1,594,058 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.00079 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00010 (1 hom.)
• Consequence: ASB10 ENST00000420175.3 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1 O:1
• Conservation: PhyloP100: -1.24
• Publications: 0 publications found

Genes affected

ASB10 (HGNC:17185): (ankyrin repeat and SOCS box containing 10) The protein encoded by this gene is a member of the ankyrin repeat and SOCS box-containing (ASB) family of proteins. The SOCS box serves to couple suppressor of cytokine signaling (SOCS) proteins and their binding partners with the elongin B and C complex, possibly targeting them for degradation. Multiple alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Dec 2008]

ASB10 Gene-Disease associations (from GenCC):

• glaucoma 1, open angle, F

  Inheritance: AD, Unknown Classification: LIMITED Submitted by: ClinGen, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BP6: Variant 7-151186460-G-A is Benign according to our data. Variant chr7-151186460-G-A is described in ClinVar as Benign. ClinVar VariationId is 99957.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.24 with no splicing effect.
• BS2: High AC in GnomAd4 at 120 AD,Unknown gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420175.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB10	NM_001142459.2	MANE Select	c.516C>T	p.Ala172Ala	synonymous	Exon 2 of 6	NP_001135931.2
	ASB10	NM_080871.4		c.471C>T	p.Ala157Ala	synonymous	Exon 2 of 6	NP_543147.2
	ASB10	NM_001142460.1		c.516C>T	p.Ala172Ala	synonymous	Exon 2 of 5	NP_001135932.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB10	ENST00000420175.3	TSL:1 MANE Select	c.516C>T	p.Ala172Ala	synonymous	Exon 2 of 6	ENSP00000391137.2
	ASB10	ENST00000275838.5	TSL:1	c.516C>T	p.Ala172Ala	synonymous	Exon 2 of 5	ENSP00000275838.1
	ASB10	ENST00000377867.7	TSL:2	c.471C>T	p.Ala157Ala	synonymous	Exon 2 of 6	ENSP00000367098.3

Frequencies

GnomAD3 genomes AF: 0.000788 AC: 120 AN: 152196 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00280

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000196

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000478

GnomAD2 exomes AF: 0.000218 AC: 46 AN: 210914 AF XY: 0.000149

Gnomad AFR exome AF: 0.00262

Gnomad AMR exome AF: 0.0000326

Gnomad ASJ exome AF: 0.000216

Gnomad EAS exome AF: 0.000384

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000324

Gnomad OTH exome AF: 0.000189

GnomAD4 exome AF: 0.0000999 AC: 144 AN: 1441744 Hom.: 1 Cov.: 31 AF XY: 0.0000880 AC XY: 63 AN XY: 715508

African (AFR) AF: 0.00308 AC: 102 AN: 33064

American (AMR) AF: 0.0000721 AC: 3 AN: 41610

Ashkenazi Jewish (ASJ) AF: 0.0000778 AC: 2 AN: 25702

East Asian (EAS) AF: 0.000311 AC: 12 AN: 38602

South Asian (SAS) AF: 0.00 AC: 0 AN: 83218

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51496

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5702

European-Non Finnish (NFE) AF: 0.00000907 AC: 10 AN: 1102694

Other (OTH) AF: 0.000251 AC: 15 AN: 59656

GnomAD4 genome AF: 0.000788 AC: 120 AN: 152314 Hom.: 0 Cov.: 33 AF XY: 0.000806 AC XY: 60 AN XY: 74470

African (AFR) AF: 0.00279 AC: 116 AN: 41564

American (AMR) AF: 0.000196 AC: 3 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.00 AC: 0 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10626

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68020

Other (OTH) AF: 0.000473 AC: 1 AN: 2114

Alfa AF: 0.000558 Hom.: 0

Bravo AF: 0.000873

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)
-	-	-	Glaucoma 1, open angle, F (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	0.17
DANN	Benign	0.86
PhyloP100		-1.2

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs104886471; hg19: chr7-150883547; COSMIC: COSV51995357; COSMIC: COSV51995357;