10-71036120-A-G

Variant names:

• chr10-71036120-A-G
• rs1891159
• ENST00000646051.1:n.392+9408A>G

Variant summary

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

The ENST00000646051.1(ENSG00000285300):​n.392+9408A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 152,092 control chromosomes in the GnomAD database, including 34,631 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 0.67 (34631 hom., cov: 32)
• Consequence: ENSG00000285300 ENST00000646051.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878
• Publications: 2 publications found

Genes affected

ENSG00000285300 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646051.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285300	ENST00000646051.1		n.392+9408A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102226 AN: 151974 Hom.: 34604 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.673 AC: 102298 AN: 152092 Hom.: 34631 Cov.: 32 AF XY: 0.665 AC XY: 49412 AN XY: 74352

African (AFR) AF: 0.697 AC: 28919 AN: 41506

American (AMR) AF: 0.567 AC: 8664 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2258 AN: 3472

East Asian (EAS) AF: 0.594 AC: 3055 AN: 5146

South Asian (SAS) AF: 0.615 AC: 2954 AN: 4806

European-Finnish (FIN) AF: 0.609 AC: 6447 AN: 10590

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.701 AC: 47686 AN: 67978

Other (OTH) AF: 0.664 AC: 1406 AN: 2116

Alfa AF: 0.679 Hom.: 31569

Bravo AF: 0.669

Asia WGS AF: 0.608 AC: 2116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.14
DANN	Benign	0.73
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs1891159; hg19: chr10-72795877;