rs10865332

chr2-62354149-C-T

Variant summary

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

The ENST00000689590.1(ENSG00000228541):n.163+57703C>T 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 0.551 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: ENST00000689590.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000689590.1	n.163+57703C>T		intron_variant, non_coding_transcript_variant

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;