rs315946

Positions:

• chr2-113136287-G-A

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 0.0941 in 152,124 control chromosomes in the GnomAD database, including 922 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 0.094 (922 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 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: 0.0943 AC: 14327 AN: 152006 Hom.: 923 Cov.: 32

Gnomad AFR AF: 0.0247

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.0871

Gnomad EAS AF: 0.0220

Gnomad SAS AF: 0.0278

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.0941 AC: 14320 AN: 152124 Hom.: 922 Cov.: 32 AF XY: 0.0913 AC XY: 6793 AN XY: 74364

Gnomad4 AFR AF: 0.0246

Gnomad4 AMR AF: 0.0664

Gnomad4 ASJ AF: 0.0871

Gnomad4 EAS AF: 0.0222

Gnomad4 SAS AF: 0.0274

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.0808

Alfa AF: 0.117 Hom.: 201

Bravo AF: 0.0867

Asia WGS AF: 0.0200 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs315946; hg19: chr2-113893864;