4-186572661-T-C

Variant names:

• chr4-186572661-T-C
• rs10030173

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.369 in 151,980 control chromosomes in the GnomAD database, including 10,836 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.37 (10836 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56018 AN: 151864 Hom.: 10820 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.381

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.369 AC: 56051 AN: 151980 Hom.: 10836 Cov.: 32 AF XY: 0.377 AC XY: 28025 AN XY: 74294

African (AFR) AF: 0.289 AC: 11987 AN: 41464

American (AMR) AF: 0.461 AC: 7032 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1166 AN: 3466

East Asian (EAS) AF: 0.478 AC: 2457 AN: 5142

South Asian (SAS) AF: 0.557 AC: 2680 AN: 4814

European-Finnish (FIN) AF: 0.424 AC: 4484 AN: 10574

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.370 AC: 25108 AN: 67950

Other (OTH) AF: 0.379 AC: 799 AN: 2106

Alfa AF: 0.366 Hom.: 20235

Bravo AF: 0.361

Asia WGS AF: 0.497 AC: 1729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.50
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs10030173; hg19: chr4-187493815;