6-93826906-T-C

Variant names:

• chr6-93826906-T-C
• rs6941459
• ENST00000751325.1:n.297+8245A>G

Variant summary

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

The ENST00000751325.1(ENSG00000297836):​n.297+8245A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 151,798 control chromosomes in the GnomAD database, including 26,274 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 0.58 (26274 hom., cov: 32)
• Consequence: ENSG00000297836 ENST00000751325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 2 publications found

Genes affected

ENSG00000297836 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.671 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
ENSG00000297836	ENST00000751325.1	n.297+8245A>G		intron_variant	Intron 1 of 4
ENSG00000297836	ENST00000751326.1	n.253+8245A>G		intron_variant	Intron 1 of 2
ENSG00000297836	ENST00000751327.1	n.246+8245A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88406 AN: 151682 Hom.: 26246 Cov.: 32

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.583 AC: 88497 AN: 151798 Hom.: 26274 Cov.: 32 AF XY: 0.584 AC XY: 43320 AN XY: 74190

African (AFR) AF: 0.678 AC: 28080 AN: 41430

American (AMR) AF: 0.525 AC: 8000 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1759 AN: 3466

East Asian (EAS) AF: 0.573 AC: 2961 AN: 5170

South Asian (SAS) AF: 0.679 AC: 3271 AN: 4820

European-Finnish (FIN) AF: 0.517 AC: 5438 AN: 10510

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37450 AN: 67836

Other (OTH) AF: 0.538 AC: 1135 AN: 2110

Alfa AF: 0.554 Hom.: 9167

Bravo AF: 0.577

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.71
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs6941459; hg19: chr6-94536624; COSMIC: COSV64445482;