rs1817567

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

ENSG00000234172 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441026.1. 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
	ENSG00000234172	ENST00000441026.1	TSL:2	n.104-1274G>A		intron	N/A
	ENSG00000234172	ENST00000828168.1		n.140-15773G>A		intron	N/A

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

African (AFR) AF: 0.0636 AC: 2624 AN: 41236

American (AMR) AF: 0.130 AC: 1972 AN: 15114

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 990 AN: 3470

East Asian (EAS) AF: 0.0581 AC: 298 AN: 5126

South Asian (SAS) AF: 0.159 AC: 759 AN: 4788

European-Finnish (FIN) AF: 0.201 AC: 2003 AN: 9956

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17557 AN: 67436

Other (OTH) AF: 0.169 AC: 354 AN: 2092

Alfa AF: 0.215 Hom.: 7464

Bravo AF: 0.166

Asia WGS AF: 0.0980 AC: 339 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.52
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1817567; hg19: chr2-184797826;