2-62536212-C-T

Variant names:

• chr2-62536212-C-T
• rs901532
• ENST00000664749.1:n.1017G>A

Variant summary

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

The ENST00000664749.1(ENSG00000226622):​n.1017G>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 0.131 in 152,196 control chromosomes in the GnomAD database, including 1,481 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 0.13 (1481 hom., cov: 32)
• Consequence: ENSG00000226622 ENST00000664749.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00
• Publications: 5 publications found

Genes affected

ENSG00000226622 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664749.1. 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
	ENSG00000226622	ENST00000664749.1		n.1017G>A		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000228541	ENST00000807713.1		n.333-27586C>T		intron	N/A
	ENSG00000228541	ENST00000807714.1		n.229-18910C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19933 AN: 152078 Hom.: 1483 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0847

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.131 AC: 19945 AN: 152196 Hom.: 1481 Cov.: 32 AF XY: 0.132 AC XY: 9832 AN XY: 74394

African (AFR) AF: 0.114 AC: 4735 AN: 41528

American (AMR) AF: 0.191 AC: 2928 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3472

East Asian (EAS) AF: 0.318 AC: 1638 AN: 5154

South Asian (SAS) AF: 0.168 AC: 810 AN: 4822

European-Finnish (FIN) AF: 0.0847 AC: 899 AN: 10608

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7953 AN: 67996

Other (OTH) AF: 0.164 AC: 347 AN: 2112

Alfa AF: 0.127 Hom.: 3438

Bravo AF: 0.140

Asia WGS AF: 0.279 AC: 969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.9
DANN	Benign	0.69
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs901532; hg19: chr2-62763347;