rs6739054

Variant names:

• chr2-11080436-A-G
• rs6739054

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 0.267 in 152,020 control chromosomes in the GnomAD database, including 6,501 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 0.27 (6501 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.42 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: 0.267 AC: 40555 AN: 151902 Hom.: 6501 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.267 AC: 40565 AN: 152020 Hom.: 6501 Cov.: 31 AF XY: 0.281 AC XY: 20842 AN XY: 74284

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.254

Alfa AF: 0.284 Hom.: 14045

Bravo AF: 0.246

Asia WGS AF: 0.422 AC: 1468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.86
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6739054; hg19: chr2-11220562;