rs2614119

Variant names:

• chr5-153909865-A-G
• rs2614119

Your query was ambiguous. Multiple possible variants found:

• chr5-153909865-A-G
• chr5-153909865-A-T

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 0.51 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.524 AC: 21740 AN: 41450

American (AMR) AF: 0.573 AC: 8762 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1680 AN: 3470

East Asian (EAS) AF: 0.627 AC: 3241 AN: 5166

South Asian (SAS) AF: 0.477 AC: 2296 AN: 4818

European-Finnish (FIN) AF: 0.553 AC: 5852 AN: 10576

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32195 AN: 67962

Other (OTH) AF: 0.515 AC: 1085 AN: 2108

Alfa AF: 0.491 Hom.: 25460

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
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs2614119; hg19: chr5-153289425;