rs10762264

Variant names:

• chr10-69217077-G-A
• rs10762264
• ENST00000450995.1:n.494-305C>T

Variant summary

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

The ENST00000450995.1(ENSG00000229261):​n.494-305C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 151,978 control chromosomes in the GnomAD database, including 26,473 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 0.58 (26473 hom., cov: 32)
• Consequence: ENSG00000229261 ENST00000450995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964
• Publications: 13 publications found

Genes affected

ENSG00000229261 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928994	NR_120648.1	n.494-305C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229261	ENST00000450995.1	n.494-305C>T		intron_variant	Intron 4 of 4	2

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87897 AN: 151860 Hom.: 26442 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.579 AC: 87974 AN: 151978 Hom.: 26473 Cov.: 32 AF XY: 0.578 AC XY: 42958 AN XY: 74270

African (AFR) AF: 0.465 AC: 19280 AN: 41426

American (AMR) AF: 0.546 AC: 8344 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1534 AN: 3464

East Asian (EAS) AF: 0.247 AC: 1277 AN: 5168

South Asian (SAS) AF: 0.568 AC: 2739 AN: 4820

European-Finnish (FIN) AF: 0.741 AC: 7821 AN: 10556

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45100 AN: 67960

Other (OTH) AF: 0.539 AC: 1136 AN: 2106

Alfa AF: 0.624 Hom.: 3784

Bravo AF: 0.554

Asia WGS AF: 0.390 AC: 1360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45
DANN	Benign	0.66
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs10762264; hg19: chr10-70976833;