rs1371552

Positions:

• chr2-223501742-A-G

Variant summary

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

The ENST00000422118.1(ENSG00000231189):​n.179-2240A>G variant causes a intron, non coding transcript 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: ENST00000422118.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105373907	XR_923952.4	n.182+2489A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000422118.1	n.179-2240A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.749

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.714

Alfa AF: 0.745 Hom.: 19156

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1371552; hg19: chr2-224366460;