6-93827537-T-C

Variant names:

• chr6-93827537-T-C
• rs1336071
• ENST00000751325.1:n.297+7614A>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+7614A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,894 control chromosomes in the GnomAD database, including 23,596 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 0.55 (23596 hom., cov: 32)
• Consequence: ENSG00000297836 ENST00000751325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 10 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 = 0.659 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+7614A>G		intron_variant	Intron 1 of 4
ENSG00000297836	ENST00000751326.1	n.253+7614A>G		intron_variant	Intron 1 of 2
ENSG00000297836	ENST00000751327.1	n.246+7614A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84053 AN: 151778 Hom.: 23578 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.554 AC: 84122 AN: 151894 Hom.: 23596 Cov.: 32 AF XY: 0.556 AC XY: 41275 AN XY: 74246

African (AFR) AF: 0.576 AC: 23866 AN: 41452

American (AMR) AF: 0.514 AC: 7844 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1758 AN: 3466

East Asian (EAS) AF: 0.577 AC: 2977 AN: 5156

South Asian (SAS) AF: 0.678 AC: 3267 AN: 4818

European-Finnish (FIN) AF: 0.517 AC: 5433 AN: 10512

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

European-Non Finnish (NFE) AF: 0.552 AC: 37475 AN: 67914

Other (OTH) AF: 0.521 AC: 1099 AN: 2110

Alfa AF: 0.533 Hom.: 9644

Bravo AF: 0.544

Asia WGS AF: 0.624 AC: 2152 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.73
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1336071; hg19: chr6-94537255; COSMIC: COSV62494147;