14-92235372-T-G

Variant names:

• chr14-92235372-T-G
• rs1742707

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 0.615 in 152,102 control chromosomes in the GnomAD database, including 30,938 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 (30938 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436
• Publications: 7 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 = 0.863 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: 0.615 AC: 93454 AN: 151984 Hom.: 30885 Cov.: 33

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.615 AC: 93567 AN: 152102 Hom.: 30938 Cov.: 33 AF XY: 0.607 AC XY: 45132 AN XY: 74322

African (AFR) AF: 0.870 AC: 36146 AN: 41526

American (AMR) AF: 0.456 AC: 6961 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1741 AN: 3472

East Asian (EAS) AF: 0.296 AC: 1527 AN: 5160

South Asian (SAS) AF: 0.521 AC: 2512 AN: 4826

European-Finnish (FIN) AF: 0.530 AC: 5581 AN: 10540

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37273 AN: 67980

Other (OTH) AF: 0.576 AC: 1219 AN: 2116

Alfa AF: 0.560 Hom.: 39884

Bravo AF: 0.620

Asia WGS AF: 0.487 AC: 1699 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.75
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs1742707; hg19: chr14-92701716;