rs4852655

Variant names:

• chr2-82008520-C-T
• rs4852655
• ENST00000843045.1:n.111-1595G>A

Variant summary

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

The ENST00000843045.1(ENSG00000231781):​n.111-1595G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,042 control chromosomes in the GnomAD database, including 13,582 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 0.40 (13582 hom., cov: 33)
• Consequence: ENSG00000231781 ENST00000843045.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.558 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.111-1595G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60876 AN: 151924 Hom.: 13574 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.401 AC: 60900 AN: 152042 Hom.: 13582 Cov.: 33 AF XY: 0.403 AC XY: 29956 AN XY: 74296

African (AFR) AF: 0.185 AC: 7683 AN: 41490

American (AMR) AF: 0.513 AC: 7837 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1459 AN: 3470

East Asian (EAS) AF: 0.575 AC: 2966 AN: 5160

South Asian (SAS) AF: 0.541 AC: 2611 AN: 4826

European-Finnish (FIN) AF: 0.424 AC: 4475 AN: 10554

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32309 AN: 67946

Other (OTH) AF: 0.440 AC: 930 AN: 2114

Alfa AF: 0.427 Hom.: 5789

Bravo AF: 0.397

Asia WGS AF: 0.553 AC: 1926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.66
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs4852655; hg19: chr2-82235644;