2-62536212-C-T

Variant summary

Our verdict is Benign. Variant got -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: ENST00000664749.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664749.1	n.1017G>A		non_coding_transcript_exon_variant	4/4

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

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.0847

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.164

Alfa AF: 0.128 Hom.: 1430

Bravo AF: 0.140

Asia WGS AF: 0.279 AC: 969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	7.9
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs901532; hg19: chr2-62763347;