rs2438083

Variant names:

• chr6-1277136-A-G
• rs2438083

Your query was ambiguous. Multiple possible variants found:

• chr6-1277136-A-G
• chr6-1277136-A-T

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 0.516 in 152,104 control chromosomes in the GnomAD database, including 22,948 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 0.52 (22948 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 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: 0.516 AC: 78412 AN: 151986 Hom.: 22890 Cov.: 33

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.516 AC: 78531 AN: 152104 Hom.: 22948 Cov.: 33 AF XY: 0.526 AC XY: 39130 AN XY: 74366

African (AFR) AF: 0.768 AC: 31874 AN: 41504

American (AMR) AF: 0.440 AC: 6728 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1447 AN: 3472

East Asian (EAS) AF: 0.830 AC: 4285 AN: 5162

South Asian (SAS) AF: 0.711 AC: 3420 AN: 4812

European-Finnish (FIN) AF: 0.464 AC: 4901 AN: 10568

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24384 AN: 67986

Other (OTH) AF: 0.505 AC: 1066 AN: 2110

Alfa AF: 0.432 Hom.: 2668

Bravo AF: 0.518

Asia WGS AF: 0.804 AC: 2790 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.6
DANN	Benign	0.27
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2438083; hg19: chr6-1277371;