rs17268364

Variant names:

• chr2-203913095-G-A
• rs17268364
• ENST00000810800.1:n.204-2194G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-203913095-G-A
• chr2-203913095-G-T

Variant summary

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

The ENST00000810800.1(ENSG00000305408):​n.204-2194G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,876 control chromosomes in the GnomAD database, including 13,833 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 0.41 (13833 hom., cov: 31)
• Consequence: ENSG00000305408 ENST00000810800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157
• Publications: 11 publications found

Genes affected

ENSG00000305408 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.649 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
ENSG00000305408	ENST00000810800.1	n.204-2194G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62912 AN: 151758 Hom.: 13842 Cov.: 31

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.414 AC: 62904 AN: 151876 Hom.: 13833 Cov.: 31 AF XY: 0.412 AC XY: 30545 AN XY: 74224

African (AFR) AF: 0.279 AC: 11554 AN: 41400

American (AMR) AF: 0.458 AC: 6981 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1766 AN: 3470

East Asian (EAS) AF: 0.308 AC: 1590 AN: 5154

South Asian (SAS) AF: 0.668 AC: 3215 AN: 4810

European-Finnish (FIN) AF: 0.344 AC: 3623 AN: 10536

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32652 AN: 67940

Other (OTH) AF: 0.473 AC: 998 AN: 2110

Alfa AF: 0.475 Hom.: 4852

Bravo AF: 0.410

Asia WGS AF: 0.511 AC: 1776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.39
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs17268364; hg19: chr2-204777818;