rs56015515

Positions:

• chr2-85498231-G-A
• chr2-85498231-G-C
• chr2-85498231-G-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 0.175 in 152,006 control chromosomes in the GnomAD database, including 2,580 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 0.18 (2580 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26649 AN: 151888 Hom.: 2579 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0396

Gnomad SAS AF: 0.0686

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.175 AC: 26661 AN: 152006 Hom.: 2580 Cov.: 32 AF XY: 0.174 AC XY: 12943 AN XY: 74300

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.0397

Gnomad4 SAS AF: 0.0693

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.182

Alfa AF: 0.164 Hom.: 729

Bravo AF: 0.166

Asia WGS AF: 0.0660 AC: 229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0020
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56015515; hg19: chr2-85725354;