11-35076646-T-C

Variant names:

• chr11-35076646-T-C
• rs387619
• ENST00000747995.1:n.137-11792T>C

Variant summary

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

The ENST00000747995.1(ENSG00000297460):​n.137-11792T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 152,132 control chromosomes in the GnomAD database, including 34,098 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 0.66 (34098 hom., cov: 32)
• Consequence: ENSG00000297460 ENST00000747995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527
• Publications: 18 publications found

Genes affected

ENSG00000297460 (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 (AFR) allele frequency at 95% confidence interval = 0.818 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
ENSG00000297460	ENST00000747995.1	n.137-11792T>C		intron_variant	Intron 2 of 4
ENSG00000297460	ENST00000747996.1	n.85-11792T>C		intron_variant	Intron 1 of 2
ENSG00000297460	ENST00000747997.1	n.84-11792T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100116 AN: 152012 Hom.: 34062 Cov.: 32

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.659 AC: 100203 AN: 152132 Hom.: 34098 Cov.: 32 AF XY: 0.662 AC XY: 49220 AN XY: 74352

African (AFR) AF: 0.825 AC: 34281 AN: 41536

American (AMR) AF: 0.664 AC: 10157 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2213 AN: 3470

East Asian (EAS) AF: 0.785 AC: 4071 AN: 5184

South Asian (SAS) AF: 0.781 AC: 3769 AN: 4826

European-Finnish (FIN) AF: 0.537 AC: 5665 AN: 10546

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37904 AN: 67960

Other (OTH) AF: 0.671 AC: 1419 AN: 2116

Alfa AF: 0.533 Hom.: 2508

Bravo AF: 0.672

Asia WGS AF: 0.770 AC: 2677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.25
DANN	Benign	0.50
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs387619; hg19: chr11-35098193;