2-19758735-G-A

Variant names:

• chr2-19758735-G-A
• rs17564315
• ENST00000810569.1:n.236-14529C>T

Variant summary

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

The ENST00000810569.1(ENSG00000305355):​n.236-14529C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,234 control chromosomes in the GnomAD database, including 1,737 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 0.15 (1737 hom., cov: 33)
• Consequence: ENSG00000305355 ENST00000810569.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43
• Publications: 7 publications found

Genes affected

ENSG00000305355 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810569.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305355	ENST00000810569.1		n.236-14529C>T		intron	N/A
	ENSG00000305355	ENST00000810570.1		n.222-8156C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22318 AN: 152116 Hom.: 1729 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.0828

Gnomad SAS AF: 0.0656

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.147 AC: 22357 AN: 152234 Hom.: 1737 Cov.: 33 AF XY: 0.143 AC XY: 10620 AN XY: 74434

African (AFR) AF: 0.137 AC: 5696 AN: 41552

American (AMR) AF: 0.142 AC: 2179 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0937 AC: 325 AN: 3470

East Asian (EAS) AF: 0.0836 AC: 432 AN: 5170

South Asian (SAS) AF: 0.0659 AC: 318 AN: 4828

European-Finnish (FIN) AF: 0.151 AC: 1598 AN: 10598

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11412 AN: 67996

Other (OTH) AF: 0.149 AC: 314 AN: 2110

Alfa AF: 0.161 Hom.: 6035

Bravo AF: 0.147

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.75
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs17564315; hg19: chr2-19958496;