7-57819147-T-C

Variant names:

• chr7-57819147-T-C
• rs6974091

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.841

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.756

Alfa AF: 0.728 Hom.: 68161

Bravo AF: 0.774

Asia WGS AF: 0.773 AC: 2691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6974091; hg19: chr7-57878853;