rs104886464

Variant names:

• chr7-151187663-G-A
• rs104886464
• NM_080871.4:c.60C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-151187663-G-A
• chr7-151187663-G-C
• chr7-151187663-G-T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Strong BP7 BS2

The NM_080871.4(ASB10):​c.60C>T​(p.Ser20Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000604 in 1,516,792 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency:
  • Genomes: 𝑓 0.0034 (3 hom., cov: 32)
  • Exomes 𝑓: 0.00029 (3 hom.)
• Consequence: ASB10 NM_080871.4 synonymous
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: -3.76
• Publications: 1 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 -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP7: Synonymous conserved (PhyloP=-3.76 with no splicing effect.
• BS2: High AC in GnomAd4 at 519 AD,Unknown gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080871.4. 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_080871.4		c.60C>T	p.Ser20Ser	synonymous	Exon 1 of 6	NP_543147.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB10	ENST00000377867.7	TSL:2	c.60C>T	p.Ser20Ser	synonymous	Exon 1 of 6	ENSP00000367098.3
	ASB10	ENST00000415615.1	TSL:4	n.60C>T		non_coding_transcript_exon	Exon 1 of 3	ENSP00000410871.1

Frequencies

GnomAD3 genomes AF: 0.00341 AC: 519 AN: 152180 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.0115

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00249

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: 0.0000147

Gnomad OTH AF: 0.000958

GnomAD2 exomes AF: 0.00109 AC: 142 AN: 130302 AF XY: 0.000754

Gnomad AFR exome AF: 0.0127

Gnomad AMR exome AF: 0.00170

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000203

Gnomad OTH exome AF: 0.00110

GnomAD4 exome AF: 0.000291 AC: 397 AN: 1364494 Hom.: 3 Cov.: 33 AF XY: 0.000240 AC XY: 160 AN XY: 667616

African (AFR) AF: 0.00825 AC: 256 AN: 31030

American (AMR) AF: 0.00176 AC: 59 AN: 33518

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22866

East Asian (EAS) AF: 0.0000567 AC: 2 AN: 35248

South Asian (SAS) AF: 0.0000134 AC: 1 AN: 74508

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47938

Middle Eastern (MID) AF: 0.000181 AC: 1 AN: 5514

European-Non Finnish (NFE) AF: 0.0000265 AC: 28 AN: 1057546

Other (OTH) AF: 0.000888 AC: 50 AN: 56326

GnomAD4 genome AF: 0.00341 AC: 519 AN: 152298 Hom.: 3 Cov.: 32 AF XY: 0.00310 AC XY: 231 AN XY: 74472

African (AFR) AF: 0.0115 AC: 478 AN: 41570

American (AMR) AF: 0.00248 AC: 38 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.00 AC: 0 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10620

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

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 68008

Other (OTH) AF: 0.000948 AC: 2 AN: 2110

Alfa AF: 0.00243 Hom.: 1

Bravo AF: 0.00406

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: not provided

Revision: no classification provided

Pathogenic	VUS	Benign	Condition
-	-	-	Glaucoma 1, open angle, F (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.53
PhyloP100		-3.8
PromoterAI		-0.035	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs104886464; hg19: chr7-150884750; COSMIC: COSV99317999; COSMIC: COSV99317999;