chr2-27745587-A-C

Variant names:

• chr2-27745587-A-C
• rs9967838
• ENST00000813446.1:n.852-7285A>C

Variant summary

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

The ENST00000813446.1(ENSG00000289326):​n.852-7285A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 150,606 control chromosomes in the GnomAD database, including 31,027 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 0.62 (31027 hom., cov: 30)
• Consequence: ENSG00000289326 ENST00000813446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 4 publications found

Genes affected

ENSG00000289326 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.746 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
ENSG00000289326	ENST00000813446.1	n.852-7285A>C		intron_variant	Intron 3 of 4
ENSG00000289326	ENST00000813447.1	n.1064-7285A>C		intron_variant	Intron 2 of 4
ENSG00000289326	ENST00000813448.1	n.1088-7285A>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.624 AC: 93987 AN: 150532 Hom.: 31035 Cov.: 30

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.624 AC: 93989 AN: 150606 Hom.: 31027 Cov.: 30 AF XY: 0.622 AC XY: 45748 AN XY: 73544

African (AFR) AF: 0.412 AC: 16782 AN: 40768

American (AMR) AF: 0.560 AC: 8472 AN: 15138

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2561 AN: 3462

East Asian (EAS) AF: 0.432 AC: 2193 AN: 5078

South Asian (SAS) AF: 0.676 AC: 3244 AN: 4798

European-Finnish (FIN) AF: 0.746 AC: 7673 AN: 10282

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.751 AC: 50927 AN: 67782

Other (OTH) AF: 0.650 AC: 1365 AN: 2100

Alfa AF: 0.644 Hom.: 4449

Bravo AF: 0.590

Asia WGS AF: 0.518 AC: 1799 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.7
DANN	Benign	0.77
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs9967838; hg19: chr2-27968454;