rs10865332

Variant names:

• chr2-62354149-C-T
• rs10865332
• ENST00000687402.2:n.196-53981C>T

Variant summary

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

The ENST00000687402.2(ENSG00000228541):​n.196-53981C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 151,750 control chromosomes in the GnomAD database, including 23,126 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 0.55 (23126 hom., cov: 32)
• Consequence: ENSG00000228541 ENST00000687402.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

Genes affected

ENSG00000228541 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.561 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
ENSG00000228541	ENST00000687402.2	n.196-53981C>T		intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000687773.2	n.200-7671C>T		intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000689590.1	n.163+57703C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83583 AN: 151634 Hom.: 23100 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.551 AC: 83664 AN: 151750 Hom.: 23126 Cov.: 32 AF XY: 0.554 AC XY: 41046 AN XY: 74150

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.536

Alfa AF: 0.557 Hom.: 47997

Bravo AF: 0.543

Asia WGS AF: 0.528 AC: 1837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.49
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10865332; hg19: chr2-62581284;