rs362408

Variant names:

• chr14-73231840-G-A
• rs362408

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;