rs10490369

Variant names:

• chr2-40955665-T-C
• rs10490369
• ENST00000753888.1:n.149+14544A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-40955665-T-C
• chr2-40955665-T-G

Variant summary

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

The ENST00000753888.1(ENSG00000298207):​n.149+14544A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0472 in 152,244 control chromosomes in the GnomAD database, including 633 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 0.047 (633 hom., cov: 32)
• Consequence: ENSG00000298207 ENST00000753888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741
• Publications: 2 publications found

Genes affected

ENSG00000298207 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374497	XR_001739421.3	n.59+14544A>G		intron_variant	Intron 1 of 3
LOC105374497	XR_001739423.1	n.59+14544A>G		intron_variant	Intron 1 of 4
LOC105374497	XR_939994.2	n.59+14544A>G		intron_variant	Intron 1 of 3
LOC105374497	XR_939995.2	n.59+14544A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298207	ENST00000753888.1	n.149+14544A>G		intron_variant	Intron 2 of 4
ENSG00000298207	ENST00000753889.1	n.149+14544A>G		intron_variant	Intron 2 of 5
ENSG00000298207	ENST00000753890.1	n.245+14544A>G		intron_variant	Intron 3 of 6
ENSG00000298207	ENST00000753891.1	n.245+14544A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0472 AC: 7175 AN: 152126 Hom.: 627 Cov.: 32

Gnomad AFR AF: 0.00931

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.0396

Gnomad FIN AF: 0.0427

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0207

Gnomad OTH AF: 0.0564

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

GnomAD4 genome AF: 0.0472 AC: 7182 AN: 152244 Hom.: 633 Cov.: 32 AF XY: 0.0524 AC XY: 3897 AN XY: 74426

African (AFR) AF: 0.00928 AC: 386 AN: 41582

American (AMR) AF: 0.195 AC: 2986 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0585 AC: 203 AN: 3468

East Asian (EAS) AF: 0.275 AC: 1416 AN: 5158

South Asian (SAS) AF: 0.0394 AC: 190 AN: 4824

European-Finnish (FIN) AF: 0.0427 AC: 453 AN: 10616

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0208 AC: 1411 AN: 68000

Other (OTH) AF: 0.0553 AC: 117 AN: 2114

Alfa AF: 0.0310 Hom.: 36

Bravo AF: 0.0622

Asia WGS AF: 0.141 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.37
DANN	Benign	0.65
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs10490369; hg19: chr2-41182805;