chr10-81803953-C-T

Variant names:

• chr10-81803953-C-T
• rs2207647
• ENST00000821630.1:n.440-9348G>A

Variant summary

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

The ENST00000821630.1(ENSG00000287358):​n.440-9348G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,984 control chromosomes in the GnomAD database, including 20,352 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 0.51 (20352 hom., cov: 32)
• Consequence: ENSG00000287358 ENST00000821630.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.663
• Publications: 4 publications found

Genes affected

ENSG00000287358 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 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
ENSG00000287358	ENST00000821630.1	n.440-9348G>A		intron_variant	Intron 3 of 4
ENSG00000287358	ENST00000821631.1	n.248-9348G>A		intron_variant	Intron 2 of 3
ENSG00000287358	ENST00000821632.1	n.304-9348G>A		intron_variant	Intron 3 of 4
ENSG00000287358	ENST00000821633.1	n.330-9348G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77907 AN: 151866 Hom.: 20340 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.513 AC: 77957 AN: 151984 Hom.: 20352 Cov.: 32 AF XY: 0.520 AC XY: 38603 AN XY: 74300

African (AFR) AF: 0.492 AC: 20401 AN: 41432

American (AMR) AF: 0.485 AC: 7414 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1480 AN: 3462

East Asian (EAS) AF: 0.782 AC: 4028 AN: 5154

South Asian (SAS) AF: 0.679 AC: 3267 AN: 4812

European-Finnish (FIN) AF: 0.584 AC: 6176 AN: 10572

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.495 AC: 33673 AN: 67960

Other (OTH) AF: 0.474 AC: 1001 AN: 2114

Alfa AF: 0.499 Hom.: 2353

Bravo AF: 0.501

Asia WGS AF: 0.690 AC: 2400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	8.9
DANN	Benign	0.49
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs2207647; hg19: chr10-83563709;