6-26255223-A-G

Variant names:

• chr6-26255223-A-G
• rs6935954
• ENST00000707189.1:n.999+131052A>G

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.999+131052A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 152,164 control chromosomes in the GnomAD database, including 40,604 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 0.72 (40604 hom., cov: 32)
• Consequence: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 22 publications found

Genes affected

ENSG00000291336 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000707189.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291336	ENST00000707189.1		n.999+131052A>G		intron	N/A
	ENSG00000291338	ENST00000707191.1		n.1000+97102A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108844 AN: 152046 Hom.: 40553 Cov.: 32

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.716 AC: 108958 AN: 152164 Hom.: 40604 Cov.: 32 AF XY: 0.723 AC XY: 53774 AN XY: 74374

African (AFR) AF: 0.908 AC: 37711 AN: 41542

American (AMR) AF: 0.702 AC: 10738 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2549 AN: 3472

East Asian (EAS) AF: 0.919 AC: 4767 AN: 5188

South Asian (SAS) AF: 0.763 AC: 3682 AN: 4828

European-Finnish (FIN) AF: 0.688 AC: 7272 AN: 10572

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39943 AN: 67950

Other (OTH) AF: 0.736 AC: 1557 AN: 2116

Alfa AF: 0.631 Hom.: 65340

Bravo AF: 0.725

Asia WGS AF: 0.782 AC: 2721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.26
DANN	Benign	0.26
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6935954;

hg19: chr6-26255451;