chr2-117776811-C-A

Variant names:

• chr2-117776811-C-A
• rs1433527
• ENST00000457110.1:n.161+8719G>T

Variant summary

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

The ENST00000457110.1(ENSG00000238207):​n.161+8719G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,768 control chromosomes in the GnomAD database, including 15,023 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 0.44 (15023 hom., cov: 31)
• Consequence: ENSG00000238207 ENST00000457110.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166
• Publications: 7 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 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.161+8719G>T		intron_variant	Intron 2 of 3	4
ENSG00000238207	ENST00000656175.1	n.167-16220G>T		intron_variant	Intron 1 of 2
ENSG00000238207	ENST00000789622.1	n.157-12329G>T		intron_variant	Intron 1 of 2
ENSG00000238207	ENST00000789623.1	n.149-16220G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66508 AN: 151650 Hom.: 15000 Cov.: 31

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.439 AC: 66579 AN: 151768 Hom.: 15023 Cov.: 31 AF XY: 0.444 AC XY: 32888 AN XY: 74152

African (AFR) AF: 0.350 AC: 14486 AN: 41344

American (AMR) AF: 0.458 AC: 6991 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1434 AN: 3468

East Asian (EAS) AF: 0.588 AC: 3032 AN: 5154

South Asian (SAS) AF: 0.402 AC: 1928 AN: 4794

European-Finnish (FIN) AF: 0.576 AC: 6070 AN: 10536

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31146 AN: 67900

Other (OTH) AF: 0.456 AC: 963 AN: 2112

Alfa AF: 0.444 Hom.: 7958

Bravo AF: 0.428

Asia WGS AF: 0.515 AC: 1789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.66
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1433527; hg19: chr2-118534387;