rs2370771

Variant names:

• chr10-32413528-C-T
• rs2370771
• ENST00000658560.2:n.1227G>A

Variant summary

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

The ENST00000658560.2(ENSG00000286409):​n.1227G>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 ENST00000658560.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 7 publications found

Genes affected

ENSG00000286409 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658560.2. 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
	ENSG00000286409	ENST00000658560.2		n.1227G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000286409	ENST00000819277.1		n.698G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000286409	ENST00000819278.1		n.1036G>A		non_coding_transcript_exon	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

African (AFR) AF: 0.663 AC: 27497 AN: 41452

American (AMR) AF: 0.377 AC: 5773 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 830 AN: 3472

East Asian (EAS) AF: 0.267 AC: 1380 AN: 5176

South Asian (SAS) AF: 0.381 AC: 1839 AN: 4822

European-Finnish (FIN) AF: 0.301 AC: 3177 AN: 10558

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15597 AN: 67980

Other (OTH) AF: 0.312 AC: 657 AN: 2108

Alfa AF: 0.282 Hom.: 22197

Bravo AF: 0.394

Asia WGS AF: 0.363 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.41
PhyloP100		0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2370771;

hg19: chr10-32702456;