rs10896450

Variant names:

• chr11-69240647-A-G
• rs10896450
• ENST00000779509.1:n.139-7714A>G

Variant summary

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

The ENST00000779509.1(ENSG00000301530):​n.139-7714A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 152,100 control chromosomes in the GnomAD database, including 23,701 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 0.54 (23701 hom., cov: 32)
• Consequence: ENSG00000301530 ENST00000779509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 27 publications found

Genes affected

ENSG00000301530 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 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
ENSG00000301530	ENST00000779509.1	n.139-7714A>G		intron_variant	Intron 1 of 3
ENSG00000301530	ENST00000779510.1	n.76+5511A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81560 AN: 151982 Hom.: 23657 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.0641

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.537 AC: 81657 AN: 152100 Hom.: 23701 Cov.: 32 AF XY: 0.529 AC XY: 39306 AN XY: 74344

African (AFR) AF: 0.727 AC: 30174 AN: 41490

American (AMR) AF: 0.401 AC: 6133 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2293 AN: 3466

East Asian (EAS) AF: 0.0635 AC: 329 AN: 5182

South Asian (SAS) AF: 0.331 AC: 1593 AN: 4810

European-Finnish (FIN) AF: 0.470 AC: 4974 AN: 10588

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34429 AN: 67954

Other (OTH) AF: 0.550 AC: 1160 AN: 2110

Alfa AF: 0.501 Hom.: 15460

Bravo AF: 0.541

Asia WGS AF: 0.310 AC: 1080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.72
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10896450; hg19: chr11-69008114;