7-151176479-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001142459.2(ASB10):c.1218+84G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00876 in 1,481,710 control chromosomes in the GnomAD database, including 1,359 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.011 (156 hom., cov: 33)
  • Exomes 𝑓: 0.0085 (1203 hom.)
• Consequence: ASB10 NM_001142459.2 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.473

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 7-151176479-C-T is Benign according to our data. Variant chr7-151176479-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1317501.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASB10	NM_001142459.2	c.1218+84G>A		intron_variant		ENST00000420175.3
ASB10	NM_001142460.1	c.1105-182G>A		intron_variant
ASB10	NM_080871.4	c.1173+84G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASB10	ENST00000420175.3	c.1218+84G>A		intron_variant		1	NM_001142459.2	P4
ASB10	ENST00000275838.5	c.1105-182G>A		intron_variant		1
ASB10	ENST00000377867.7	c.1173+84G>A		intron_variant		2		A1

Frequencies

GnomAD3 genomes AF: 0.0113 AC: 1724 AN: 152132 Hom.: 158 Cov.: 33

Gnomad AFR AF: 0.00179

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0171

Gnomad ASJ AF: 0.00922

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.00849

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000500

Gnomad OTH AF: 0.0105

GnomAD4 exome AF: 0.00846 AC: 11252 AN: 1329460 Hom.: 1203 Cov.: 29 AF XY: 0.00842 AC XY: 5477 AN XY: 650130

Gnomad4 AFR exome AF: 0.000819

Gnomad4 AMR exome AF: 0.0331

Gnomad4 ASJ exome AF: 0.00705

Gnomad4 EAS exome AF: 0.253

Gnomad4 SAS exome AF: 0.00367

Gnomad4 FIN exome AF: 0.000236

Gnomad4 NFE exome AF: 0.000215

Gnomad4 OTH exome AF: 0.0144

GnomAD4 genome AF: 0.0113 AC: 1722 AN: 152250 Hom.: 156 Cov.: 33 AF XY: 0.0123 AC XY: 912 AN XY: 74432

Gnomad4 AFR AF: 0.00178

Gnomad4 AMR AF: 0.0171

Gnomad4 ASJ AF: 0.00922

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.00871

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000500

Gnomad4 OTH AF: 0.0104

Alfa AF: 0.00281 Hom.: 2

Bravo AF: 0.0139

Asia WGS AF: 0.0910 AC: 316 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 25, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.25
Dann	Benign	0.64

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

Publications

LitVar

Other links and lift over

dbSNP: rs4726004; hg19: chr7-150873566; COSMIC: COSV52002001; COSMIC: COSV52002001;