rs6745746

Positions:

• chr2-112852467-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 0.393 in 151,888 control chromosomes in the GnomAD database, including 12,199 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 0.39 (12199 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 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: 0.394 AC: 59728 AN: 151768 Hom.: 12205 Cov.: 31

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.393 AC: 59722 AN: 151888 Hom.: 12199 Cov.: 31 AF XY: 0.390 AC XY: 28947 AN XY: 74204

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.393

Alfa AF: 0.421 Hom.: 1726

Bravo AF: 0.391

Asia WGS AF: 0.333 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.1
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6745746; hg19: chr2-113610044;