14-92935748-C-G

Variant names:

• chr14-92935748-C-G
• rs875395

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 0.589 in 152,124 control chromosomes in the GnomAD database, including 26,841 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 0.59 (26841 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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: 0.589 AC: 89595 AN: 152006 Hom.: 26831 Cov.: 33

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.673

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.589 AC: 89642 AN: 152124 Hom.: 26841 Cov.: 33 AF XY: 0.590 AC XY: 43892 AN XY: 74386

African (AFR) AF: 0.642 AC: 26647 AN: 41486

American (AMR) AF: 0.534 AC: 8165 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2064 AN: 3468

East Asian (EAS) AF: 0.754 AC: 3900 AN: 5172

South Asian (SAS) AF: 0.708 AC: 3416 AN: 4828

European-Finnish (FIN) AF: 0.555 AC: 5872 AN: 10574

Middle Eastern (MID) AF: 0.690 AC: 200 AN: 290

European-Non Finnish (NFE) AF: 0.555 AC: 37717 AN: 67988

Other (OTH) AF: 0.607 AC: 1285 AN: 2116

Alfa AF: 0.422 Hom.: 1068

Bravo AF: 0.585

Asia WGS AF: 0.715 AC: 2489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.27
DANN	Benign	0.64
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs875395; hg19: chr14-93402093;