chr7-46133306-C-T

Variant names:

• chr7-46133306-C-T
• rs6950179

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 0.489 in 151,990 control chromosomes in the GnomAD database, including 18,967 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 0.49 (18967 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.621 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: 0.488 AC: 74181 AN: 151872 Hom.: 18941 Cov.: 32

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.489 AC: 74251 AN: 151990 Hom.: 18967 Cov.: 32 AF XY: 0.494 AC XY: 36692 AN XY: 74270

African (AFR) AF: 0.627 AC: 26002 AN: 41450

American (AMR) AF: 0.495 AC: 7558 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1488 AN: 3472

East Asian (EAS) AF: 0.606 AC: 3128 AN: 5158

South Asian (SAS) AF: 0.564 AC: 2715 AN: 4814

European-Finnish (FIN) AF: 0.450 AC: 4757 AN: 10564

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27187 AN: 67952

Other (OTH) AF: 0.461 AC: 972 AN: 2110

Alfa AF: 0.376 Hom.: 1631

Bravo AF: 0.495

Asia WGS AF: 0.574 AC: 1997 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	0.60
DANN	Benign	0.64
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs6950179; hg19: chr7-46172904;