chr7-41947526-G-A

Variant names:

• chr7-41947526-G-A
• rs17171989

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 0.402 in 151,742 control chromosomes in the GnomAD database, including 13,884 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 0.40 (13884 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.625 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: 0.401 AC: 60837 AN: 151624 Hom.: 13843 Cov.: 31

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.402 AC: 60939 AN: 151742 Hom.: 13884 Cov.: 31 AF XY: 0.395 AC XY: 29308 AN XY: 74170

African (AFR) AF: 0.632 AC: 26074 AN: 41282

American (AMR) AF: 0.293 AC: 4465 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1088 AN: 3462

East Asian (EAS) AF: 0.401 AC: 2058 AN: 5132

South Asian (SAS) AF: 0.313 AC: 1502 AN: 4806

European-Finnish (FIN) AF: 0.274 AC: 2896 AN: 10552

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21686 AN: 67932

Other (OTH) AF: 0.392 AC: 828 AN: 2110

Alfa AF: 0.339 Hom.: 4887

Bravo AF: 0.412

Asia WGS AF: 0.422 AC: 1471 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	0.13
DANN	Benign	0.37
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs17171989; hg19: chr7-41987124;