rs10496384

Variant names:

• chr2-104353103-A-G
• rs10496384
• ENST00000758996.1:n.238+40722T>C

Variant summary

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

The ENST00000758996.1(ENSG00000298919):​n.238+40722T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0963 in 149,826 control chromosomes in the GnomAD database, including 2,015 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 0.096 (2015 hom., cov: 28)
• Consequence: ENSG00000298919 ENST00000758996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903
• Publications: 0 publications found

Genes affected

ENSG00000298919 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298919	ENST00000758996.1	n.238+40722T>C		intron_variant	Intron 2 of 2
ENSG00000298919	ENST00000758997.1	n.266+40722T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0961 AC: 14385 AN: 149736 Hom.: 2010 Cov.: 28

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.0513

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.00259

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.00535

Gnomad OTH AF: 0.0719

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

GnomAD4 genome AF: 0.0963 AC: 14426 AN: 149826 Hom.: 2015 Cov.: 28 AF XY: 0.0937 AC XY: 6844 AN XY: 73076

African (AFR) AF: 0.303 AC: 12275 AN: 40544

American (AMR) AF: 0.0813 AC: 1227 AN: 15088

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3456

East Asian (EAS) AF: 0.0516 AC: 261 AN: 5054

South Asian (SAS) AF: 0.0141 AC: 67 AN: 4742

European-Finnish (FIN) AF: 0.00259 AC: 26 AN: 10026

Middle Eastern (MID) AF: 0.0347 AC: 10 AN: 288

European-Non Finnish (NFE) AF: 0.00535 AC: 362 AN: 67654

Other (OTH) AF: 0.0743 AC: 154 AN: 2074

Alfa AF: 0.0443 Hom.: 263

Bravo AF: 0.114

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.45
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs10496384; hg19: chr2-104969561;