6-25944983-A-G

Variant names:

• chr6-25944983-A-G
• rs2051541

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 0.471 in 152,018 control chromosomes in the GnomAD database, including 17,555 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 0.47 (17555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 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: 0.471 AC: 71519 AN: 151900 Hom.: 17545 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.471 AC: 71561 AN: 152018 Hom.: 17555 Cov.: 32 AF XY: 0.476 AC XY: 35360 AN XY: 74302

African (AFR) AF: 0.358 AC: 14864 AN: 41462

American (AMR) AF: 0.495 AC: 7552 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1416 AN: 3470

East Asian (EAS) AF: 0.776 AC: 4008 AN: 5162

South Asian (SAS) AF: 0.449 AC: 2165 AN: 4818

European-Finnish (FIN) AF: 0.585 AC: 6174 AN: 10554

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.498 AC: 33854 AN: 67972

Other (OTH) AF: 0.476 AC: 1003 AN: 2108

Alfa AF: 0.490 Hom.: 25053

Bravo AF: 0.464

Asia WGS AF: 0.580 AC: 2016 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.1
DANN	Benign	0.80
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2051541; hg19: chr6-25945211;