chr7-57819147-T-C

Variant names:

• chr7-57819147-T-C
• rs6974091

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 0.765 in 151,852 control chromosomes in the GnomAD database, including 44,683 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 0.76 (44683 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116065 AN: 151732 Hom.: 44645 Cov.: 31

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.765 AC: 116155 AN: 151852 Hom.: 44683 Cov.: 31 AF XY: 0.768 AC XY: 56981 AN XY: 74160

African (AFR) AF: 0.810 AC: 33579 AN: 41438

American (AMR) AF: 0.824 AC: 12573 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2384 AN: 3468

East Asian (EAS) AF: 0.841 AC: 4266 AN: 5072

South Asian (SAS) AF: 0.753 AC: 3619 AN: 4808

European-Finnish (FIN) AF: 0.785 AC: 8280 AN: 10542

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 49001 AN: 67948

Other (OTH) AF: 0.756 AC: 1594 AN: 2108

Alfa AF: 0.738 Hom.: 120029

Bravo AF: 0.774

Asia WGS AF: 0.773 AC: 2691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.26
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6974091; hg19: chr7-57878853;