6-26288975-T-C

Variant names:

• chr6-26288975-T-C
• rs6939589
• ENST00000707189.1:n.999+164804T>C

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.999+164804T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,990 control chromosomes in the GnomAD database, including 23,036 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 0.54 (23036 hom., cov: 32)
• Consequence: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.89
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 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+164804T>C		intron	N/A
	ENSG00000291338	ENST00000707191.1		n.1000+130854T>C		intron	N/A
	ENSG00000287050	ENST00000771288.1		n.533-488A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81792 AN: 151874 Hom.: 23030 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.538 AC: 81838 AN: 151990 Hom.: 23036 Cov.: 32 AF XY: 0.552 AC XY: 41021 AN XY: 74272

African (AFR) AF: 0.405 AC: 16795 AN: 41428

American (AMR) AF: 0.592 AC: 9042 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2247 AN: 3472

East Asian (EAS) AF: 0.866 AC: 4476 AN: 5170

South Asian (SAS) AF: 0.743 AC: 3579 AN: 4818

European-Finnish (FIN) AF: 0.677 AC: 7138 AN: 10542

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36684 AN: 67960

Other (OTH) AF: 0.571 AC: 1205 AN: 2110

Alfa AF: 0.542 Hom.: 48726

Bravo AF: 0.525

Asia WGS AF: 0.734 AC: 2554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.15
DANN	Benign	0.23
PhyloP100		-3.9

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: rs6939589;

hg19: chr6-26289203;

COSMIC: COSV56805729;