rs362408

chr14-73231840-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 0.0903 in 152,252 control chromosomes in the GnomAD database, including 732 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 0.090 (732 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 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: 0.0905 AC: 13762 AN: 152134 Hom.: 736 Cov.: 32

Gnomad AFR AF: 0.0522

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.0684

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.0903 AC: 13754 AN: 152252 Hom.: 732 Cov.: 32 AF XY: 0.0889 AC XY: 6615 AN XY: 74442

Gnomad4 AFR AF: 0.0521

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.0650

Gnomad4 FIN AF: 0.0684

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.127

Alfa AF: 0.0967 Hom.: 183

Bravo AF: 0.0933

Asia WGS AF: 0.131 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.1
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs362408; hg19: chr14-73698548;