2-67491158-C-T

Variant names:

• chr2-67491158-C-T
• rs7584345
• ENST00000833659.1:n.374-276G>A

Variant summary

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

The ENST00000833659.1(ENSG00000308373):​n.374-276G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,082 control chromosomes in the GnomAD database, including 31,974 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 0.64 (31974 hom., cov: 34)
• Consequence: ENSG00000308373 ENST00000833659.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195
• Publications: 4 publications found

Genes affected

ENSG00000308373 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.693 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
ENSG00000308373	ENST00000833659.1	n.374-276G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97791 AN: 151962 Hom.: 31961 Cov.: 34

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.643 AC: 97844 AN: 152082 Hom.: 31974 Cov.: 34 AF XY: 0.639 AC XY: 47494 AN XY: 74338

African (AFR) AF: 0.604 AC: 25060 AN: 41460

American (AMR) AF: 0.496 AC: 7571 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2379 AN: 3470

East Asian (EAS) AF: 0.597 AC: 3082 AN: 5164

South Asian (SAS) AF: 0.674 AC: 3247 AN: 4814

European-Finnish (FIN) AF: 0.637 AC: 6732 AN: 10572

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47475 AN: 68010

Other (OTH) AF: 0.654 AC: 1380 AN: 2110

Alfa AF: 0.678 Hom.: 157940

Bravo AF: 0.624

Asia WGS AF: 0.636 AC: 2209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.67
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs7584345; hg19: chr2-67718290;