rs6918981

Variant names:

• chr6-34270737-G-A
• rs6918981
• ENST00000586726.3:n.137-8403G>A

Variant summary

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

The ENST00000586726.3(ENSG00000225339):​n.137-8403G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 152,052 control chromosomes in the GnomAD database, including 38,550 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 0.70 (38550 hom., cov: 32)
• Consequence: ENSG00000225339 ENST00000586726.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 27 publications found

Genes affected

ENSG00000225339 (HGNC:58176):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.843 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
ENSG00000225339	ENST00000586726.3	n.137-8403G>A		intron_variant	Intron 1 of 2	5
ENSG00000225339	ENST00000659015.2	n.147-7171G>A		intron_variant	Intron 1 of 3
ENSG00000225339	ENST00000732777.1	n.121-7171G>A		intron_variant	Intron 1 of 1
ENSG00000225339	ENST00000732778.1	n.104-2641G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105702 AN: 151934 Hom.: 38551 Cov.: 32

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.695 AC: 105724 AN: 152052 Hom.: 38550 Cov.: 32 AF XY: 0.699 AC XY: 51909 AN XY: 74288

African (AFR) AF: 0.462 AC: 19141 AN: 41444

American (AMR) AF: 0.649 AC: 9908 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2541 AN: 3468

East Asian (EAS) AF: 0.850 AC: 4389 AN: 5166

South Asian (SAS) AF: 0.864 AC: 4172 AN: 4826

European-Finnish (FIN) AF: 0.808 AC: 8530 AN: 10562

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54658 AN: 68008

Other (OTH) AF: 0.706 AC: 1492 AN: 2112

Alfa AF: 0.770 Hom.: 189930

Bravo AF: 0.669

Asia WGS AF: 0.789 AC: 2741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.52
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6918981; hg19: chr6-34238514;