rs7141276

chr14-34665980-A-Gchr14-34665980-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.483 in 151,984 control chromosomes in the GnomAD database, including 19,019 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 0.48 (19019 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73322 AN: 151866 Hom.: 18991 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.483 AC: 73404 AN: 151984 Hom.: 19019 Cov.: 32 AF XY: 0.483 AC XY: 35863 AN XY: 74288

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.570

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.449

Alfa AF: 0.412 Hom.: 7352

Bravo AF: 0.505

Asia WGS AF: 0.478 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.6
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7141276; hg19: chr14-35135186;