rs6739883

Positions:

• chr2-113156735-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 0.163 in 152,138 control chromosomes in the GnomAD database, including 2,149 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 0.16 (2149 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.981

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 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: 0.163 AC: 24840 AN: 152020 Hom.: 2147 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.0368

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.163 AC: 24841 AN: 152138 Hom.: 2149 Cov.: 32 AF XY: 0.164 AC XY: 12231 AN XY: 74362

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.0367

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.164

Alfa AF: 0.176 Hom.: 3256

Bravo AF: 0.153

Asia WGS AF: 0.142 AC: 493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6739883; hg19: chr2-113914312;