6-88136230-T-C

Variant names:

• chr6-88136230-T-C
• rs806365
• ENST00000756364.1:n.128+10633T>C

Variant summary

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

The ENST00000756364.1(ENSG00000298549):​n.128+10633T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 151,998 control chromosomes in the GnomAD database, including 28,644 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 0.61 (28644 hom., cov: 31)
• Consequence: ENSG00000298549 ENST00000756364.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 20 publications found

Genes affected

ENSG00000298549 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 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
ENSG00000298549	ENST00000756364.1	n.128+10633T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92707 AN: 151880 Hom.: 28627 Cov.: 31

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.610 AC: 92771 AN: 151998 Hom.: 28644 Cov.: 31 AF XY: 0.612 AC XY: 45438 AN XY: 74288

African (AFR) AF: 0.683 AC: 28325 AN: 41466

American (AMR) AF: 0.592 AC: 9029 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1753 AN: 3462

East Asian (EAS) AF: 0.614 AC: 3174 AN: 5170

South Asian (SAS) AF: 0.581 AC: 2797 AN: 4810

European-Finnish (FIN) AF: 0.626 AC: 6612 AN: 10566

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39263 AN: 67952

Other (OTH) AF: 0.576 AC: 1215 AN: 2110

Alfa AF: 0.583 Hom.: 109840

Bravo AF: 0.609

Asia WGS AF: 0.602 AC: 2094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	5.5
DANN	Benign	0.70
PhyloP100		-0.089

Splicing

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

Other links and lift over

dbSNP: rs806365; hg19: chr6-88845949; COSMIC: COSV65673256;