rs12622351

Variant names:

• chr2-155871058-T-C
• rs12622351
• ENST00000799383.1:n.876+35302A>G

Variant summary

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

The ENST00000799383.1(ENSG00000304068):​n.876+35302A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,058 control chromosomes in the GnomAD database, including 2,389 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 0.17 (2389 hom., cov: 32)
• Consequence: ENSG00000304068 ENST00000799383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 0 publications found

Genes affected

ENSG00000304068 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373703	XR_001739749.2	n.638-30074A>G		intron_variant	Intron 4 of 7
LOC105373703	XR_001739750.2	n.638-30074A>G		intron_variant	Intron 4 of 5
LOC105373703	XR_001739751.2	n.638-30074A>G		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304068	ENST00000799383.1	n.876+35302A>G		intron_variant	Intron 6 of 8
ENSG00000304068	ENST00000799384.1	n.693+35302A>G		intron_variant	Intron 1 of 4
ENSG00000304068	ENST00000799387.1	n.118-3871A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25633 AN: 151940 Hom.: 2384 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.169 AC: 25670 AN: 152058 Hom.: 2389 Cov.: 32 AF XY: 0.169 AC XY: 12548 AN XY: 74336

African (AFR) AF: 0.232 AC: 9615 AN: 41478

American (AMR) AF: 0.133 AC: 2033 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 479 AN: 3470

East Asian (EAS) AF: 0.249 AC: 1288 AN: 5172

South Asian (SAS) AF: 0.172 AC: 828 AN: 4824

European-Finnish (FIN) AF: 0.122 AC: 1294 AN: 10580

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9644 AN: 67954

Other (OTH) AF: 0.170 AC: 358 AN: 2112

Alfa AF: 0.156 Hom.: 255

Bravo AF: 0.170

Asia WGS AF: 0.194 AC: 674 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.5
DANN	Benign	0.74
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs12622351; hg19: chr2-156727570;