rs1371552

Variant names:

• chr2-223501742-A-G
• rs1371552
• ENST00000422118.1:n.179-2240A>G

Variant summary

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

The ENST00000422118.1(ENSG00000231189):​n.179-2240A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,072 control chromosomes in the GnomAD database, including 41,201 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 0.73 (41201 hom., cov: 32)
• Consequence: ENSG00000231189 ENST00000422118.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 2 publications found

Genes affected

ENSG00000231189 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373907	NR_187972.1	n.204+2489A>G		intron_variant	Intron 2 of 4
LOC105373907	NR_187973.1	n.204+2489A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231189	ENST00000422118.1	n.179-2240A>G		intron_variant	Intron 2 of 2	3
ENSG00000303770	ENST00000797088.1	n.189-18098T>C		intron_variant	Intron 2 of 3
ENSG00000303770	ENST00000797089.1	n.43-18098T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111587 AN: 151954 Hom.: 41167 Cov.: 32

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.734 AC: 111663 AN: 152072 Hom.: 41201 Cov.: 32 AF XY: 0.733 AC XY: 54449 AN XY: 74314

African (AFR) AF: 0.749 AC: 31082 AN: 41484

American (AMR) AF: 0.639 AC: 9756 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2519 AN: 3470

East Asian (EAS) AF: 0.671 AC: 3464 AN: 5160

South Asian (SAS) AF: 0.674 AC: 3249 AN: 4820

European-Finnish (FIN) AF: 0.749 AC: 7908 AN: 10562

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.754 AC: 51246 AN: 67992

Other (OTH) AF: 0.714 AC: 1509 AN: 2114

Alfa AF: 0.746 Hom.: 21349

Bravo AF: 0.727

Asia WGS AF: 0.675 AC: 2343 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.39
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs1371552; hg19: chr2-224366460;