chr2-62354149-C-T

Variant names:

• chr2-62354149-C-T
• rs10865332
• ENST00000687402.3:n.200-53981C>T

Variant summary

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

The ENST00000687402.3(ENSG00000228541):​n.200-53981C>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 ENST00000687402.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 6 publications found

Genes affected

ENSG00000228541 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687402.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228541	ENST00000687402.3		n.200-53981C>T		intron	N/A
	ENSG00000228541	ENST00000687773.2		n.200-7671C>T		intron	N/A
	ENSG00000228541	ENST00000689590.2		n.198+57703C>T		intron	N/A

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

African (AFR) AF: 0.531 AC: 21935 AN: 41336

American (AMR) AF: 0.547 AC: 8338 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1788 AN: 3466

East Asian (EAS) AF: 0.472 AC: 2437 AN: 5166

South Asian (SAS) AF: 0.579 AC: 2782 AN: 4802

European-Finnish (FIN) AF: 0.596 AC: 6253 AN: 10500

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.566 AC: 38417 AN: 67928

Other (OTH) AF: 0.536 AC: 1129 AN: 2106

Alfa AF: 0.555 Hom.: 73329

Bravo AF: 0.543

Asia WGS AF: 0.528 AC: 1837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.49
DANN	Benign	0.63
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10865332; hg19: chr2-62581284;