2-235220307-A-G

Variant names:

• chr2-235220307-A-G
• rs1991705
• ENST00000762435.1:n.127-16335T>C

Variant summary

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

The ENST00000762435.1(ENSG00000299301):​n.127-16335T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 152,218 control chromosomes in the GnomAD database, including 58,409 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 0.87 (58409 hom., cov: 33)
• Consequence: ENSG00000299301 ENST00000762435.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.58
• Publications: 5 publications found

Genes affected

ENSG00000299301 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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
ENSG00000299301	ENST00000762435.1	n.127-16335T>C		intron_variant	Intron 1 of 2
ENSG00000299301	ENST00000762436.1	n.101+7336T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132636 AN: 152100 Hom.: 58363 Cov.: 33

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.872 AC: 132739 AN: 152218 Hom.: 58409 Cov.: 33 AF XY: 0.872 AC XY: 64901 AN XY: 74424

African (AFR) AF: 0.759 AC: 31524 AN: 41526

American (AMR) AF: 0.832 AC: 12721 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3091 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5164 AN: 5170

South Asian (SAS) AF: 0.912 AC: 4403 AN: 4826

European-Finnish (FIN) AF: 0.938 AC: 9948 AN: 10608

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.927 AC: 63042 AN: 68004

Other (OTH) AF: 0.867 AC: 1830 AN: 2110

Alfa AF: 0.888 Hom.: 92315

Bravo AF: 0.859

Asia WGS AF: 0.940 AC: 3265 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	0.015
DANN	Benign	0.39
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs1991705; hg19: chr2-236128951;