rs6918981

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000225339 (HGNC:58176):

ACMG classification

Verdict is Benign. Variant got -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	ENST00000659015.1	n.91-7171G>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

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.808

Gnomad4 NFE AF: 0.804

Gnomad4 OTH AF: 0.706

Alfa AF: 0.784 Hom.: 87296

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6918981; hg19: chr6-34238514;