rs1817567

Variant names:

• chr2-183933099-G-A
• rs1817567
• ENST00000441026.1:n.104-1274G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000441026.1(ENSG00000234172):​n.104-1274G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 150,420 control chromosomes in the GnomAD database, including 3,747 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 0.18 (3747 hom., cov: 31)
• Consequence: ENSG00000234172 ENST00000441026.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

Genes affected

ENSG00000234172 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 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
ENSG00000234172	ENST00000441026.1	n.104-1274G>A		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.178 AC: 26776 AN: 150312 Hom.: 3749 Cov.: 31

Gnomad AFR AF: 0.0637

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.0582

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.178 AC: 26771 AN: 150420 Hom.: 3747 Cov.: 31 AF XY: 0.172 AC XY: 12633 AN XY: 73300

Gnomad4 AFR AF: 0.0636

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.0581

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.169

Alfa AF: 0.237 Hom.: 5601

Bravo AF: 0.166

Asia WGS AF: 0.0980 AC: 339 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1817567; hg19: chr2-184797826;