rs11256463

Variant names:

• chr10-10049303-G-A
• rs11256463
• ENST00000738164.1:n.195-41365G>A

Variant summary

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

The ENST00000738164.1(ENSG00000296323):​n.195-41365G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,942 control chromosomes in the GnomAD database, including 12,163 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 0.40 (12163 hom., cov: 32)
• Consequence: ENSG00000296323 ENST00000738164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• Publications: 2 publications found

Genes affected

ENSG00000296323 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 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
ENSG00000296323	ENST00000738164.1	n.195-41365G>A		intron_variant	Intron 2 of 8
ENSG00000296323	ENST00000738165.1	n.222-41365G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60069 AN: 151822 Hom.: 12147 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.396 AC: 60123 AN: 151942 Hom.: 12163 Cov.: 32 AF XY: 0.401 AC XY: 29775 AN XY: 74268

African (AFR) AF: 0.385 AC: 15948 AN: 41436

American (AMR) AF: 0.311 AC: 4740 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1366 AN: 3464

East Asian (EAS) AF: 0.445 AC: 2290 AN: 5148

South Asian (SAS) AF: 0.411 AC: 1974 AN: 4808

European-Finnish (FIN) AF: 0.507 AC: 5334 AN: 10526

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27038 AN: 67982

Other (OTH) AF: 0.391 AC: 826 AN: 2110

Alfa AF: 0.387 Hom.: 14283

Bravo AF: 0.378

Asia WGS AF: 0.375 AC: 1301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.44
PhyloP100		-0.086

Splicing

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

Other links and lift over

dbSNP: rs11256463; hg19: chr10-10091266;