4-98771141-T-C

Variant names:

• chr4-98771141-T-C
• rs10007831

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 0.584 in 152,026 control chromosomes in the GnomAD database, including 26,918 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 0.58 (26918 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.781
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.856 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: 0.583 AC: 88629 AN: 151910 Hom.: 26871 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.584 AC: 88742 AN: 152026 Hom.: 26918 Cov.: 32 AF XY: 0.591 AC XY: 43924 AN XY: 74320

African (AFR) AF: 0.696 AC: 28871 AN: 41476

American (AMR) AF: 0.615 AC: 9388 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1980 AN: 3470

East Asian (EAS) AF: 0.877 AC: 4537 AN: 5174

South Asian (SAS) AF: 0.766 AC: 3689 AN: 4816

European-Finnish (FIN) AF: 0.532 AC: 5621 AN: 10556

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32920 AN: 67952

Other (OTH) AF: 0.562 AC: 1184 AN: 2108

Alfa AF: 0.501 Hom.: 9440

Bravo AF: 0.590

Asia WGS AF: 0.811 AC: 2820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.44
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs10007831; hg19: chr4-99692292;