chr7-95325551-C-T

Variant names:

• chr7-95325551-C-T
• rs854573

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 0.717 in 152,060 control chromosomes in the GnomAD database, including 39,757 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 0.72 (39757 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 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: 0.717 AC: 108917 AN: 151942 Hom.: 39722 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.717 AC: 109005 AN: 152060 Hom.: 39757 Cov.: 32 AF XY: 0.723 AC XY: 53707 AN XY: 74318

African (AFR) AF: 0.575 AC: 23831 AN: 41446

American (AMR) AF: 0.802 AC: 12268 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2809 AN: 3470

East Asian (EAS) AF: 0.869 AC: 4494 AN: 5174

South Asian (SAS) AF: 0.718 AC: 3461 AN: 4822

European-Finnish (FIN) AF: 0.781 AC: 8255 AN: 10564

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51349 AN: 67976

Other (OTH) AF: 0.754 AC: 1595 AN: 2114

Alfa AF: 0.753 Hom.: 111869

Bravo AF: 0.716

Asia WGS AF: 0.800 AC: 2784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.19
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs854573; hg19: chr7-94954863;