rs2250266

Variant names:

• chr10-121138399-G-A
• rs2250266
• ENST00000741064.1:n.94-19050C>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000741064.1(ENSG00000296663):​n.94-19050C>T variant causes a intron change. The variant allele was found at a frequency of 0.488 in 152,080 control chromosomes in the GnomAD database, including 20,507 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.49 (20507 hom., cov: 32)
• Consequence: ENSG00000296663 ENST00000741064.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.07
• Publications: 1 publications found

Genes affected

ENSG00000296663 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902515	XR_007062317.1	n.168-19050C>T		intron_variant	Intron 1 of 1
LOC124902515	XR_007062318.1	n.159-19050C>T		intron_variant	Intron 1 of 1
LOC105378522	XR_946379.3	n.356+8576G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296663	ENST00000741064.1	n.94-19050C>T		intron_variant	Intron 1 of 1
ENSG00000296663	ENST00000741065.1	n.85-19050C>T		intron_variant	Intron 1 of 1
ENSG00000296663	ENST00000741066.1	n.238-19050C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74205 AN: 151962 Hom.: 20508 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.488 AC: 74228 AN: 152080 Hom.: 20507 Cov.: 32 AF XY: 0.489 AC XY: 36364 AN XY: 74324

African (AFR) AF: 0.231 AC: 9571 AN: 41484

American (AMR) AF: 0.459 AC: 7005 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2200 AN: 3470

East Asian (EAS) AF: 0.378 AC: 1953 AN: 5162

South Asian (SAS) AF: 0.760 AC: 3667 AN: 4826

European-Finnish (FIN) AF: 0.615 AC: 6494 AN: 10566

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41413 AN: 67984

Other (OTH) AF: 0.516 AC: 1089 AN: 2112

Alfa AF: 0.564 Hom.: 61626

Bravo AF: 0.455

Asia WGS AF: 0.531 AC: 1845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Uncertain	-0.070
CADD	Benign	21
DANN	Benign	0.81
PhyloP100		6.1

Splicing

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

Other links and lift over

dbSNP: rs2250266; hg19: chr10-122897913;