rs4141217

Variant names:

• chr7-95356868-C-T
• rs4141217

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 0.541 in 152,044 control chromosomes in the GnomAD database, including 22,837 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 0.54 (22837 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82193 AN: 151926 Hom.: 22783 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.541 AC: 82305 AN: 152044 Hom.: 22837 Cov.: 32 AF XY: 0.555 AC XY: 41259 AN XY: 74318

African (AFR) AF: 0.573 AC: 23759 AN: 41458

American (AMR) AF: 0.614 AC: 9375 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1452 AN: 3470

East Asian (EAS) AF: 0.783 AC: 4048 AN: 5170

South Asian (SAS) AF: 0.690 AC: 3324 AN: 4818

European-Finnish (FIN) AF: 0.627 AC: 6615 AN: 10558

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.470 AC: 31944 AN: 67978

Other (OTH) AF: 0.521 AC: 1101 AN: 2114

Alfa AF: 0.492 Hom.: 23955

Bravo AF: 0.541

Asia WGS AF: 0.738 AC: 2563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.2
DANN	Benign	0.93
PhyloP100		-0.46
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: rs4141217; hg19: chr7-94986180;