2-210287981-A-G

Variant names:

• chr2-210287981-A-G
• rs867342
• ENST00000795993.1:n.388+8120A>G

Variant summary

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

The ENST00000795993.1(ENSG00000279317):​n.388+8120A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 152,000 control chromosomes in the GnomAD database, including 17,349 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 0.48 (17349 hom., cov: 32)
• Consequence: ENSG00000279317 ENST00000795993.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 3 publications found

Genes affected

ENSG00000279317 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000795993.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000279317	ENST00000795993.1		n.388+8120A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72324 AN: 151880 Hom.: 17301 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.477 AC: 72432 AN: 152000 Hom.: 17349 Cov.: 32 AF XY: 0.483 AC XY: 35835 AN XY: 74256

African (AFR) AF: 0.421 AC: 17478 AN: 41478

American (AMR) AF: 0.568 AC: 8667 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2084 AN: 3470

East Asian (EAS) AF: 0.453 AC: 2342 AN: 5168

South Asian (SAS) AF: 0.541 AC: 2610 AN: 4822

European-Finnish (FIN) AF: 0.504 AC: 5319 AN: 10544

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32189 AN: 67942

Other (OTH) AF: 0.499 AC: 1053 AN: 2110

Alfa AF: 0.462 Hom.: 8036

Bravo AF: 0.477

Asia WGS AF: 0.525 AC: 1823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	4.1
DANN	Benign	0.87
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs867342;

hg19: chr2-211152705;