2-190735698-T-G

Variant names:

• chr2-190735698-T-G
• rs1263125
• ENST00000676095.2:n.263+3565A>C

Variant summary

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

The ENST00000676095.2(ENSG00000228509):​n.263+3565A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,960 control chromosomes in the GnomAD database, including 20,823 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 0.52 (20823 hom., cov: 32)
• Consequence: ENSG00000228509 ENST00000676095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398
• Publications: 1 publications found

Genes affected

ENSG00000228509 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000676095.2. 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
	ENSG00000228509	ENST00000676095.2		n.263+3565A>C		intron	N/A
	ENSG00000228509	ENST00000676386.1		n.703+3565A>C		intron	N/A
	ENSG00000228509	ENST00000691949.3		n.535+3565A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78536 AN: 151842 Hom.: 20799 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.517 AC: 78604 AN: 151960 Hom.: 20823 Cov.: 32 AF XY: 0.514 AC XY: 38154 AN XY: 74270

African (AFR) AF: 0.439 AC: 18208 AN: 41436

American (AMR) AF: 0.627 AC: 9572 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1982 AN: 3466

East Asian (EAS) AF: 0.690 AC: 3561 AN: 5162

South Asian (SAS) AF: 0.453 AC: 2180 AN: 4814

European-Finnish (FIN) AF: 0.413 AC: 4354 AN: 10548

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36878 AN: 67948

Other (OTH) AF: 0.537 AC: 1132 AN: 2108

Alfa AF: 0.497 Hom.: 5780

Bravo AF: 0.535

Asia WGS AF: 0.566 AC: 1967 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.70
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs1263125; hg19: chr2-191600424;