chr2-40955665-T-C

Variant names:

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000753888.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298207	ENST00000753888.1		n.149+14544A>G		intron	N/A
	ENSG00000298207	ENST00000753889.1		n.149+14544A>G		intron	N/A
	ENSG00000298207	ENST00000753890.1		n.245+14544A>G		intron	N/A

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 v4.9

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;