rs4902642

chr14-68743482-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.371 in 151,950 control chromosomes in the GnomAD database, including 10,933 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 0.37 (10933 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56286 AN: 151832 Hom.: 10924 Cov.: 31

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.371 AC: 56318 AN: 151950 Hom.: 10933 Cov.: 31 AF XY: 0.374 AC XY: 27758 AN XY: 74272

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.369

Alfa AF: 0.405 Hom.: 29067

Bravo AF: 0.348

Asia WGS AF: 0.388 AC: 1348 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	9.3
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4902642; hg19: chr14-69210199;