11-63018963-C-T

Variant names:

• chr11-63018963-C-T
• rs10792369
• ENST00000782248.1:n.847-6942C>T

Variant summary

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

The ENST00000782248.1(ENSG00000301851):​n.847-6942C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 151,974 control chromosomes in the GnomAD database, including 28,042 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 0.59 (28042 hom., cov: 31)
• Consequence: ENSG00000301851 ENST00000782248.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 2 publications found

Genes affected

ENSG00000301851 (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 (NFE) allele frequency at 95% confidence interval = 0.679 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
ENSG00000301851	ENST00000782248.1	n.847-6942C>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90147 AN: 151856 Hom.: 28046 Cov.: 31

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.593 AC: 90168 AN: 151974 Hom.: 28042 Cov.: 31 AF XY: 0.594 AC XY: 44153 AN XY: 74288

African (AFR) AF: 0.403 AC: 16700 AN: 41438

American (AMR) AF: 0.611 AC: 9342 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2428 AN: 3470

East Asian (EAS) AF: 0.567 AC: 2926 AN: 5164

South Asian (SAS) AF: 0.638 AC: 3073 AN: 4818

European-Finnish (FIN) AF: 0.673 AC: 7101 AN: 10548

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.684 AC: 46460 AN: 67952

Other (OTH) AF: 0.608 AC: 1282 AN: 2108

Alfa AF: 0.647 Hom.: 105660

Bravo AF: 0.578

Asia WGS AF: 0.577 AC: 2006 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	0.41
DANN	Benign	0.42
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10792369; hg19: chr11-62786435;