2-117770496-A-G

Variant names:

• chr2-117770496-A-G
• rs204832
• ENST00000457110.1:n.162-9905T>C

Variant summary

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

The ENST00000457110.1(ENSG00000238207):​n.162-9905T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 152,154 control chromosomes in the GnomAD database, including 56,332 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 0.86 (56332 hom., cov: 31)
• Consequence: ENSG00000238207 ENST00000457110.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 3 publications found

Genes affected

ENSG00000238207 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.955 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
ENSG00000238207	ENST00000457110.1	n.162-9905T>C		intron_variant	Intron 2 of 3	4
ENSG00000238207	ENST00000656175.1	n.167-9905T>C		intron_variant	Intron 1 of 2
ENSG00000238207	ENST00000789622.1	n.157-6014T>C		intron_variant	Intron 1 of 2
ENSG00000238207	ENST00000789623.1	n.149-9905T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.857 AC: 130293 AN: 152036 Hom.: 56272 Cov.: 31

Gnomad AFR AF: 0.963

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.852

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

GnomAD4 genome AF: 0.857 AC: 130419 AN: 152154 Hom.: 56332 Cov.: 31 AF XY: 0.856 AC XY: 63692 AN XY: 74376

African (AFR) AF: 0.963 AC: 40011 AN: 41538

American (AMR) AF: 0.782 AC: 11944 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2883 AN: 3472

East Asian (EAS) AF: 0.739 AC: 3815 AN: 5162

South Asian (SAS) AF: 0.831 AC: 4010 AN: 4826

European-Finnish (FIN) AF: 0.833 AC: 8805 AN: 10576

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56068 AN: 67986

Other (OTH) AF: 0.856 AC: 1804 AN: 2108

Alfa AF: 0.793 Hom.: 3060

Bravo AF: 0.854

Asia WGS AF: 0.831 AC: 2890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.53
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs204832; hg19: chr2-118528072;