ENST00000805101.1:n.686-10290T>C

Variant names:

• chr2-136218685-T-C
• rs882300
• ENST00000805101.1:n.686-10290T>C

Variant summary

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

The ENST00000805101.1(ENSG00000304642):​n.686-10290T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 151,988 control chromosomes in the GnomAD database, including 33,302 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 0.65 (33302 hom., cov: 32)
• Consequence: ENSG00000304642 ENST00000805101.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736
• Publications: 35 publications found

Genes affected

ENSG00000304642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805101.1. 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
	ENSG00000304642	ENST00000805101.1		n.686-10290T>C		intron	N/A
	ENSG00000304642	ENST00000805103.1		n.179+4218T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99013 AN: 151870 Hom.: 33246 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.652 AC: 99128 AN: 151988 Hom.: 33302 Cov.: 32 AF XY: 0.656 AC XY: 48712 AN XY: 74266

African (AFR) AF: 0.729 AC: 30216 AN: 41466

American (AMR) AF: 0.786 AC: 12013 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3008 AN: 3470

East Asian (EAS) AF: 0.786 AC: 4071 AN: 5182

South Asian (SAS) AF: 0.796 AC: 3835 AN: 4816

European-Finnish (FIN) AF: 0.470 AC: 4949 AN: 10526

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38700 AN: 67938

Other (OTH) AF: 0.728 AC: 1533 AN: 2106

Alfa AF: 0.616 Hom.: 110804

Bravo AF: 0.674

Asia WGS AF: 0.806 AC: 2800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		-0.74

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: rs882300;

hg19: chr2-136976255;