chr14-94360731-C-T

Variant names:

• chr14-94360731-C-T
• rs2749527

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 0.42 in 152,042 control chromosomes in the GnomAD database, including 15,876 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 0.42 (15876 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.628 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: 0.420 AC: 63780 AN: 151924 Hom.: 15868 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.388

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.420 AC: 63789 AN: 152042 Hom.: 15876 Cov.: 32 AF XY: 0.424 AC XY: 31485 AN XY: 74304

African (AFR) AF: 0.154 AC: 6383 AN: 41480

American (AMR) AF: 0.617 AC: 9421 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1434 AN: 3468

East Asian (EAS) AF: 0.646 AC: 3342 AN: 5172

South Asian (SAS) AF: 0.362 AC: 1741 AN: 4810

European-Finnish (FIN) AF: 0.503 AC: 5310 AN: 10566

Middle Eastern (MID) AF: 0.397 AC: 115 AN: 290

European-Non Finnish (NFE) AF: 0.512 AC: 34772 AN: 67968

Other (OTH) AF: 0.435 AC: 918 AN: 2112

Alfa AF: 0.485 Hom.: 21081

Bravo AF: 0.422

Asia WGS AF: 0.494 AC: 1719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.43
PhyloP100		0.039

Splicing

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

Other links and lift over

dbSNP: rs2749527; hg19: chr14-94827068;