rs6734238

Variant names:

• chr2-113083453-A-G
• rs6734238

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.39 in 151,974 control chromosomes in the GnomAD database, including 12,068 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 (12068 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239
• Publications: 73 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 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: 0.390 AC: 59196 AN: 151856 Hom.: 12042 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.0685

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.390 AC: 59268 AN: 151974 Hom.: 12068 Cov.: 32 AF XY: 0.382 AC XY: 28396 AN XY: 74312

African (AFR) AF: 0.448 AC: 18545 AN: 41402

American (AMR) AF: 0.353 AC: 5385 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1411 AN: 3464

East Asian (EAS) AF: 0.0684 AC: 354 AN: 5172

South Asian (SAS) AF: 0.343 AC: 1651 AN: 4816

European-Finnish (FIN) AF: 0.306 AC: 3231 AN: 10560

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27208 AN: 67976

Other (OTH) AF: 0.412 AC: 871 AN: 2112

Alfa AF: 0.392 Hom.: 36688

Bravo AF: 0.396

Asia WGS AF: 0.273 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.29
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs6734238; hg19: chr2-113841030;