rs2438083

Positions:

• chr6-1277136-A-G
• chr6-1277136-A-T

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 0.516 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.830

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.505

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2438083; hg19: chr6-1277371;