rs1918615

Variant names:

• chr2-140040174-A-G
• rs1918615

Your query was ambiguous. Multiple possible variants found:

• chr2-140040174-A-G
• chr2-140040174-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 0.455 in 151,922 control chromosomes in the GnomAD database, including 16,402 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 0.45 (16402 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.588 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: 0.454 AC: 68979 AN: 151804 Hom.: 16380 Cov.: 31

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.455 AC: 69053 AN: 151922 Hom.: 16402 Cov.: 31 AF XY: 0.460 AC XY: 34105 AN XY: 74218

African (AFR) AF: 0.594 AC: 24604 AN: 41434

American (AMR) AF: 0.425 AC: 6477 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1266 AN: 3470

East Asian (EAS) AF: 0.565 AC: 2913 AN: 5152

South Asian (SAS) AF: 0.460 AC: 2210 AN: 4808

European-Finnish (FIN) AF: 0.428 AC: 4513 AN: 10546

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25777 AN: 67952

Other (OTH) AF: 0.427 AC: 898 AN: 2102

Alfa AF: 0.410 Hom.: 4545

Bravo AF: 0.460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.083
DANN	Benign	0.45
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1918615; hg19: chr2-140797743;