rs7141857

Variant names:

• chr14-84197944-T-C
• rs7141857

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 0.583 in 151,800 control chromosomes in the GnomAD database, including 26,295 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 0.58 (26295 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 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: 0.583 AC: 88409 AN: 151682 Hom.: 26279 Cov.: 30

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.583 AC: 88461 AN: 151800 Hom.: 26295 Cov.: 30 AF XY: 0.583 AC XY: 43214 AN XY: 74186

African (AFR) AF: 0.499 AC: 20660 AN: 41396

American (AMR) AF: 0.625 AC: 9535 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2399 AN: 3472

East Asian (EAS) AF: 0.799 AC: 4109 AN: 5144

South Asian (SAS) AF: 0.712 AC: 3427 AN: 4810

European-Finnish (FIN) AF: 0.474 AC: 4988 AN: 10520

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41101 AN: 67892

Other (OTH) AF: 0.647 AC: 1363 AN: 2108

Alfa AF: 0.595 Hom.: 8659

Bravo AF: 0.594

Asia WGS AF: 0.734 AC: 2549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.51
PhyloP100		0.079

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7141857;

hg19: chr14-84664288;