rs2614119

chr5-153909865-A-Gchr5-153909865-A-T

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 0.51 in 152,040 control chromosomes in the GnomAD database, including 19,912 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 0.51 (19912 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 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: 0.510 AC: 77425 AN: 151922 Hom.: 19886 Cov.: 32

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.510 AC: 77486 AN: 152040 Hom.: 19912 Cov.: 32 AF XY: 0.513 AC XY: 38163 AN XY: 74328

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.515

Alfa AF: 0.489 Hom.: 19496

Bravo AF: 0.519

Asia WGS AF: 0.538 AC: 1872 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
Cadd	Benign	12
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2614119; hg19: chr5-153289425;