rs17198432

Variant names:

• chr2-175524333-C-A
• rs17198432
• ENST00000807627.1:n.223-33710C>A

Variant summary

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

The ENST00000807627.1(ENSG00000305006):​n.223-33710C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0903 in 152,188 control chromosomes in the GnomAD database, including 820 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 0.090 (820 hom., cov: 32)
• Consequence: ENSG00000305006 ENST00000807627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 6 publications found

Genes affected

ENSG00000305006 (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 (AMR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807627.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305006	ENST00000807627.1		n.223-33710C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0903 AC: 13738 AN: 152070 Hom.: 821 Cov.: 32

Gnomad AFR AF: 0.0259

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0667

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0903 AC: 13739 AN: 152188 Hom.: 820 Cov.: 32 AF XY: 0.0888 AC XY: 6604 AN XY: 74396

African (AFR) AF: 0.0259 AC: 1075 AN: 41544

American (AMR) AF: 0.142 AC: 2169 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 382 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5180

South Asian (SAS) AF: 0.103 AC: 497 AN: 4818

European-Finnish (FIN) AF: 0.0667 AC: 707 AN: 10600

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8289 AN: 67980

Other (OTH) AF: 0.101 AC: 213 AN: 2114

Alfa AF: 0.113 Hom.: 186

Bravo AF: 0.0938

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.71
DANN	Benign	0.73
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs17198432; hg19: chr2-176389061;