rs2048874

Variant names:

• chr2-112766390-C-T
• rs2048874
• ENST00000762706.1:n.305+1812C>T

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.305+1812C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,184 control chromosomes in the GnomAD database, including 866 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 0.10 (866 hom., cov: 32)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 11 publications found

Genes affected

ENSG00000299339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.147 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
ENSG00000299339	ENST00000762706.1	n.305+1812C>T		intron_variant	Intron 1 of 3
ENSG00000299339	ENST00000762707.1	n.400+1812C>T		intron_variant	Intron 1 of 2
ENSG00000299339	ENST00000762708.1	n.166+1522C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15383 AN: 152066 Hom.: 861 Cov.: 32

Gnomad AFR AF: 0.0824

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0872

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.101 AC: 15396 AN: 152184 Hom.: 866 Cov.: 32 AF XY: 0.100 AC XY: 7440 AN XY: 74400

African (AFR) AF: 0.0826 AC: 3428 AN: 41516

American (AMR) AF: 0.0870 AC: 1331 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 387 AN: 3472

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5180

South Asian (SAS) AF: 0.156 AC: 751 AN: 4820

European-Finnish (FIN) AF: 0.0859 AC: 909 AN: 10576

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8234 AN: 68004

Other (OTH) AF: 0.116 AC: 246 AN: 2114

Alfa AF: 0.117 Hom.: 2089

Bravo AF: 0.0991

Asia WGS AF: 0.0760 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.96
DANN	Benign	0.59
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs2048874; hg19: chr2-113523967;