2-81922490-T-G

Variant names:

• chr2-81922490-T-G
• rs10520308
• ENST00000843045.1:n.304-328A>C

Variant summary

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

The ENST00000843045.1(ENSG00000231781):​n.304-328A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 148,162 control chromosomes in the GnomAD database, including 2,360 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 0.18 (2360 hom., cov: 27)
• Consequence: ENSG00000231781 ENST00000843045.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.699
• Publications: 3 publications found

Genes affected

ENSG00000231781 (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 (NFE) allele frequency at 95% confidence interval = 0.199 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
ENSG00000231781	ENST00000843045.1	n.304-328A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26178 AN: 148044 Hom.: 2355 Cov.: 27

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0510

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.219

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.177 AC: 26189 AN: 148162 Hom.: 2360 Cov.: 27 AF XY: 0.174 AC XY: 12547 AN XY: 72016

African (AFR) AF: 0.152 AC: 6081 AN: 40100

American (AMR) AF: 0.170 AC: 2496 AN: 14656

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 641 AN: 3438

East Asian (EAS) AF: 0.0511 AC: 249 AN: 4874

South Asian (SAS) AF: 0.164 AC: 757 AN: 4618

European-Finnish (FIN) AF: 0.171 AC: 1695 AN: 9906

Middle Eastern (MID) AF: 0.215 AC: 61 AN: 284

European-Non Finnish (NFE) AF: 0.202 AC: 13620 AN: 67326

Other (OTH) AF: 0.193 AC: 397 AN: 2058

Alfa AF: 0.191 Hom.: 1395

Bravo AF: 0.172

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.95
DANN	Benign	0.74
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs10520308; hg19: chr2-82149614;