chr7-154902677-C-T

Variant names:

• chr7-154902677-C-T
• rs2002865

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 0.827 in 152,234 control chromosomes in the GnomAD database, including 52,283 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 0.83 (52283 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.909 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: 0.827 AC: 125837 AN: 152116 Hom.: 52238 Cov.: 32

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.827 AC: 125943 AN: 152234 Hom.: 52283 Cov.: 32 AF XY: 0.826 AC XY: 61448 AN XY: 74424

African (AFR) AF: 0.917 AC: 38076 AN: 41544

American (AMR) AF: 0.831 AC: 12705 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2771 AN: 3470

East Asian (EAS) AF: 0.741 AC: 3822 AN: 5156

South Asian (SAS) AF: 0.762 AC: 3673 AN: 4818

European-Finnish (FIN) AF: 0.808 AC: 8568 AN: 10606

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53621 AN: 68026

Other (OTH) AF: 0.816 AC: 1726 AN: 2114

Alfa AF: 0.806 Hom.: 135072

Bravo AF: 0.834

Asia WGS AF: 0.802 AC: 2787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.7
DANN	Benign	0.18
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs2002865; hg19: chr7-154694387;