chr2-112964119-A-G

Variant names:

• chr2-112964119-A-G
• rs6758386

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 0.562 in 152,016 control chromosomes in the GnomAD database, including 24,927 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 0.56 (24927 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 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: 0.562 AC: 85389 AN: 151896 Hom.: 24903 Cov.: 31

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.562 AC: 85462 AN: 152016 Hom.: 24927 Cov.: 31 AF XY: 0.563 AC XY: 41870 AN XY: 74314

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.529

Alfa AF: 0.377 Hom.: 970

Bravo AF: 0.573

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6758386; hg19: chr2-113721696; COSMIC: COSV60092958;