rs7149938

Positions:

• chr14-68871059-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;