chr7-91669846-C-T

Variant names:

• chr7-91669846-C-T
• rs2974129

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 0.526 in 151,898 control chromosomes in the GnomAD database, including 22,054 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 0.53 (22054 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.445
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79903 AN: 151780 Hom.: 22047 Cov.: 30

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.526 AC: 79923 AN: 151898 Hom.: 22054 Cov.: 30 AF XY: 0.523 AC XY: 38855 AN XY: 74252

African (AFR) AF: 0.370 AC: 15298 AN: 41400

American (AMR) AF: 0.610 AC: 9310 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1507 AN: 3470

East Asian (EAS) AF: 0.419 AC: 2153 AN: 5140

South Asian (SAS) AF: 0.426 AC: 2055 AN: 4820

European-Finnish (FIN) AF: 0.573 AC: 6046 AN: 10544

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41768 AN: 67960

Other (OTH) AF: 0.519 AC: 1094 AN: 2106

Alfa AF: 0.583 Hom.: 110893

Bravo AF: 0.522

Asia WGS AF: 0.443 AC: 1544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.7
DANN	Benign	0.39
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs2974129; hg19: chr7-91299161;