10-90270862-G-T

Variant names:

• chr10-90270862-G-T
• rs10509597
• ENST00000749546.1:n.228-2446C>A

Variant summary

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

The ENST00000749546.1(ENSG00000297645):​n.228-2446C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,032 control chromosomes in the GnomAD database, including 1,498 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 0.13 (1498 hom., cov: 32)
• Consequence: ENSG00000297645 ENST00000749546.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 1 publications found

Genes affected

ENSG00000297645 (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 = 0.17 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
ENSG00000297645	ENST00000749546.1	n.228-2446C>A		intron_variant	Intron 1 of 2
ENSG00000297655	ENST00000749800.1	n.67+17964C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20077 AN: 151914 Hom.: 1498 Cov.: 32

Gnomad AFR AF: 0.0962

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.000967

Gnomad SAS AF: 0.0658

Gnomad FIN AF: 0.0890

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.132 AC: 20071 AN: 152032 Hom.: 1498 Cov.: 32 AF XY: 0.127 AC XY: 9454 AN XY: 74320

African (AFR) AF: 0.0961 AC: 3991 AN: 41530

American (AMR) AF: 0.124 AC: 1887 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 682 AN: 3466

East Asian (EAS) AF: 0.000970 AC: 5 AN: 5156

South Asian (SAS) AF: 0.0653 AC: 315 AN: 4826

European-Finnish (FIN) AF: 0.0890 AC: 943 AN: 10594

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11721 AN: 67902

Other (OTH) AF: 0.145 AC: 306 AN: 2104

Alfa AF: 0.154 Hom.: 4091

Bravo AF: 0.133

Asia WGS AF: 0.0340 AC: 117 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.41
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs10509597; hg19: chr10-92030619;