7-153006311-C-T

Variant names:

• chr7-153006311-C-T
• rs520556

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 0.66 in 152,104 control chromosomes in the GnomAD database, including 37,488 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 0.66 (37488 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 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: 0.660 AC: 100358 AN: 151986 Hom.: 37486 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.660 AC: 100370 AN: 152104 Hom.: 37488 Cov.: 32 AF XY: 0.670 AC XY: 49793 AN XY: 74364

African (AFR) AF: 0.283 AC: 11743 AN: 41448

American (AMR) AF: 0.797 AC: 12190 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 2605 AN: 3472

East Asian (EAS) AF: 0.945 AC: 4884 AN: 5170

South Asian (SAS) AF: 0.822 AC: 3963 AN: 4822

European-Finnish (FIN) AF: 0.854 AC: 9042 AN: 10590

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.787 AC: 53526 AN: 67994

Other (OTH) AF: 0.689 AC: 1456 AN: 2114

Alfa AF: 0.741 Hom.: 141358

Bravo AF: 0.643

Asia WGS AF: 0.842 AC: 2927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.60
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs520556; hg19: chr7-152703396;