rs2370771

Variant names:

• chr10-32413528-C-T
• rs2370771
• ENST00000658560.1:n.1166G>A

Variant summary

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

The ENST00000658560.1(ENSG00000286409):​n.1166G>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 0.376 in 152,068 control chromosomes in the GnomAD database, including 13,474 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 0.38 (13474 hom., cov: 32)
• Consequence: ENSG00000286409 ENST00000658560.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

ENSG00000286409 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 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
ENSG00000286409	ENST00000658560.1	n.1166G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57118 AN: 151950 Hom.: 13436 Cov.: 32

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.376 AC: 57216 AN: 152068 Hom.: 13474 Cov.: 32 AF XY: 0.381 AC XY: 28304 AN XY: 74322

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.312

Alfa AF: 0.259 Hom.: 7764

Bravo AF: 0.394

Asia WGS AF: 0.363 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2370771; hg19: chr10-32702456;