chr7-50264865-C-T

Variant names:

• chr7-50264865-C-T
• rs1456896

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 0.667 in 151,966 control chromosomes in the GnomAD database, including 34,332 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 0.67 (34332 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469
• Publications: 75 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.794 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: 0.667 AC: 101324 AN: 151850 Hom.: 34298 Cov.: 30

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.667 AC: 101412 AN: 151966 Hom.: 34332 Cov.: 30 AF XY: 0.672 AC XY: 49893 AN XY: 74286

African (AFR) AF: 0.602 AC: 24927 AN: 41414

American (AMR) AF: 0.754 AC: 11523 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2450 AN: 3472

East Asian (EAS) AF: 0.399 AC: 2048 AN: 5138

South Asian (SAS) AF: 0.815 AC: 3927 AN: 4816

European-Finnish (FIN) AF: 0.711 AC: 7514 AN: 10562

Middle Eastern (MID) AF: 0.784 AC: 229 AN: 292

European-Non Finnish (NFE) AF: 0.690 AC: 46886 AN: 67964

Other (OTH) AF: 0.665 AC: 1402 AN: 2108

Alfa AF: 0.677 Hom.: 130236

Bravo AF: 0.657

Asia WGS AF: 0.687 AC: 2388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.36
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1456896; hg19: chr7-50304461;