rs310597

Variant names:

• chr7-151175959-A-G
• rs310597
• NM_001142459.2:c.*8T>C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001142459.2(ASB10):​c.*8T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 1,003,206 control chromosomes in the GnomAD database, including 78,330 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.46 (17471 hom., cov: 33)
  • Exomes 𝑓: 0.37 (60859 hom.)
• Consequence: ASB10 NM_001142459.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.340
• Publications: 3 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: Unknown, AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), ClinGen

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 7-151175959-A-G is Benign according to our data. Variant chr7-151175959-A-G is described in ClinVar as Benign. ClinVar VariationId is 1221472.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142459.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB10	NM_001142459.2	MANE Select	c.*8T>C		3_prime_UTR	Exon 6 of 6	NP_001135931.2	Q8WXI3-1
	ASB10	NM_080871.4		c.*8T>C		3_prime_UTR	Exon 6 of 6	NP_543147.2	Q8WXI3-3
	ASB10	NM_001142460.1		c.*8T>C		3_prime_UTR	Exon 5 of 5	NP_001135932.2	Q8WXI3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB10	ENST00000420175.3	TSL:1 MANE Select	c.*8T>C		3_prime_UTR	Exon 6 of 6	ENSP00000391137.2	Q8WXI3-1
	ASB10	ENST00000275838.5	TSL:1	c.*8T>C		3_prime_UTR	Exon 5 of 5	ENSP00000275838.1	Q8WXI3-2
	ASB10	ENST00000968508.1		c.*38T>C		3_prime_UTR	Exon 6 of 6	ENSP00000638567.1

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69551 AN: 151948 Hom.: 17444 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.450

GnomAD4 exome AF: 0.373 AC: 317345 AN: 851140 Hom.: 60859 Cov.: 11 AF XY: 0.369 AC XY: 156909 AN XY: 424696

African (AFR) AF: 0.682 AC: 12502 AN: 18336

American (AMR) AF: 0.334 AC: 5670 AN: 16984

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 6619 AN: 15802

East Asian (EAS) AF: 0.338 AC: 10156 AN: 30088

South Asian (SAS) AF: 0.291 AC: 15352 AN: 52728

European-Finnish (FIN) AF: 0.410 AC: 12280 AN: 29948

Middle Eastern (MID) AF: 0.377 AC: 1028 AN: 2726

European-Non Finnish (NFE) AF: 0.369 AC: 238365 AN: 645536

Other (OTH) AF: 0.394 AC: 15373 AN: 38992

GnomAD4 genome AF: 0.458 AC: 69625 AN: 152066 Hom.: 17471 Cov.: 33 AF XY: 0.454 AC XY: 33739 AN XY: 74334

African (AFR) AF: 0.678 AC: 28141 AN: 41482

American (AMR) AF: 0.377 AC: 5761 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1429 AN: 3472

East Asian (EAS) AF: 0.350 AC: 1803 AN: 5148

South Asian (SAS) AF: 0.299 AC: 1444 AN: 4824

European-Finnish (FIN) AF: 0.413 AC: 4370 AN: 10580

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25319 AN: 67960

Other (OTH) AF: 0.449 AC: 947 AN: 2108

Alfa AF: 0.402 Hom.: 43344

Bravo AF: 0.469

Asia WGS AF: 0.347 AC: 1210 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.78
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism (auto)

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: rs310597; hg19: chr7-150873046; COSMIC: COSV51995139; COSMIC: COSV51995139;