rs7149938

Variant names:

• chr14-68871059-G-A
• rs7149938

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 0.69 in 151,460 control chromosomes in the GnomAD database, including 36,226 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 0.69 (36226 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.758 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: 0.690 AC: 104486 AN: 151340 Hom.: 36195 Cov.: 30

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.690 AC: 104562 AN: 151460 Hom.: 36226 Cov.: 30 AF XY: 0.691 AC XY: 51125 AN XY: 74000

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.695

Alfa AF: 0.690 Hom.: 4469

Bravo AF: 0.695

Asia WGS AF: 0.702 AC: 2438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.5
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7149938; hg19: chr14-69337776;