rs6739883

Variant names:

• chr2-113156735-G-A
• rs6739883

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;