rs1370523

chr2-145765158-C-Achr2-145765158-C-G

Variant summary

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

The ENST00000651680.1(ENSG00000286225):n.1192C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 151,792 control chromosomes in the GnomAD database, including 22,880 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 0.54 (22880 hom., cov: 31)
• Consequence: ENST00000651680.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389

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 (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124908059	XR_007088682.1	n.559C>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651680.1	n.1192C>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82286 AN: 151674 Hom.: 22867 Cov.: 31

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.542 AC: 82334 AN: 151792 Hom.: 22880 Cov.: 31 AF XY: 0.547 AC XY: 40583 AN XY: 74148

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.545

Alfa AF: 0.499 Hom.: 33308

Bravo AF: 0.544

Asia WGS AF: 0.667 AC: 2320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.1
Dann	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1370523; hg19: chr2-146522726;