rs1341001

Variant names:

• chr14-94896359-A-G
• rs1341001

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 0.621 in 152,084 control chromosomes in the GnomAD database, including 30,573 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 0.62 (30573 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 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: 0.621 AC: 94406 AN: 151966 Hom.: 30526 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.621 AC: 94513 AN: 152084 Hom.: 30573 Cov.: 32 AF XY: 0.616 AC XY: 45834 AN XY: 74350

African (AFR) AF: 0.739 AC: 30664 AN: 41484

American (AMR) AF: 0.456 AC: 6968 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2261 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1388 AN: 5168

South Asian (SAS) AF: 0.386 AC: 1857 AN: 4814

European-Finnish (FIN) AF: 0.696 AC: 7368 AN: 10580

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 42021 AN: 67962

Other (OTH) AF: 0.616 AC: 1300 AN: 2112

Alfa AF: 0.605 Hom.: 79390

Bravo AF: 0.607

Asia WGS AF: 0.418 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.7
DANN	Benign	0.48
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1341001; hg19: chr14-95362696;