rs2749529

Variant names:

• chr14-94354122-T-A
• rs2749529

Your query was ambiguous. Multiple possible variants found:

• chr14-94354122-T-A
• chr14-94354122-T-C

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 0.458 in 152,022 control chromosomes in the GnomAD database, including 18,360 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 0.46 (18360 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.638 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: 0.458 AC: 69601 AN: 151904 Hom.: 18354 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.458 AC: 69614 AN: 152022 Hom.: 18360 Cov.: 32 AF XY: 0.461 AC XY: 34216 AN XY: 74274

African (AFR) AF: 0.195 AC: 8112 AN: 41494

American (AMR) AF: 0.649 AC: 9917 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1531 AN: 3472

East Asian (EAS) AF: 0.646 AC: 3339 AN: 5170

South Asian (SAS) AF: 0.366 AC: 1764 AN: 4822

European-Finnish (FIN) AF: 0.540 AC: 5670 AN: 10498

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37736 AN: 67968

Other (OTH) AF: 0.477 AC: 1006 AN: 2108

Alfa AF: 0.503 Hom.: 2605

Bravo AF: 0.462

Asia WGS AF: 0.502 AC: 1748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.39
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs2749529; hg19: chr14-94820459;