rs2901286

Variant names:

• chr10-121141109-C-A
• rs2901286
• ENST00000741064.1:n.94-21760G>T

Variant summary

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

The ENST00000741064.1(ENSG00000296663):​n.94-21760G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0205 in 152,290 control chromosomes in the GnomAD database, including 149 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 0.021 (149 hom., cov: 33)
• Consequence: ENSG00000296663 ENST00000741064.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.827
• Publications: 7 publications found

Genes affected

ENSG00000296663 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902515	XR_007062317.1	n.168-21760G>T		intron_variant	Intron 1 of 1
LOC124902515	XR_007062318.1	n.159-21760G>T		intron_variant	Intron 1 of 1
LOC105378522	XR_946379.3	n.357-10939C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296663	ENST00000741064.1	n.94-21760G>T		intron_variant	Intron 1 of 1
ENSG00000296663	ENST00000741065.1	n.85-21760G>T		intron_variant	Intron 1 of 1
ENSG00000296663	ENST00000741066.1	n.238-21760G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0205 AC: 3123 AN: 152172 Hom.: 149 Cov.: 33

Gnomad AFR AF: 0.00374

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0461

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.0246

Gnomad FIN AF: 0.0247

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.0211

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

GnomAD4 genome AF: 0.0205 AC: 3128 AN: 152290 Hom.: 149 Cov.: 33 AF XY: 0.0232 AC XY: 1728 AN XY: 74462

African (AFR) AF: 0.00373 AC: 155 AN: 41554

American (AMR) AF: 0.0467 AC: 715 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00317 AC: 11 AN: 3472

East Asian (EAS) AF: 0.209 AC: 1083 AN: 5182

South Asian (SAS) AF: 0.0246 AC: 119 AN: 4830

European-Finnish (FIN) AF: 0.0247 AC: 262 AN: 10606

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0108 AC: 733 AN: 68026

Other (OTH) AF: 0.0208 AC: 44 AN: 2112

Alfa AF: 0.0188 Hom.: 387

Bravo AF: 0.0232

Asia WGS AF: 0.0790 AC: 273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.5
DANN	Benign	0.42
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs2901286; hg19: chr10-122900623;