rs1515114

Variant names:

• chr2-226233671-A-G
• rs1515114

Your query was ambiguous. Multiple possible variants found:

• chr2-226233671-A-G
• chr2-226233671-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 0.461 in 152,020 control chromosomes in the GnomAD database, including 16,396 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 0.46 (16396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.722

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.531 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: 0.461 AC: 70033 AN: 151902 Hom.: 16374 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.461 AC: 70089 AN: 152020 Hom.: 16396 Cov.: 32 AF XY: 0.457 AC XY: 33966 AN XY: 74312

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.494

Alfa AF: 0.489 Hom.: 37239

Bravo AF: 0.468

Asia WGS AF: 0.582 AC: 2025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	9.9
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1515114; hg19: chr2-227098387;