2-134722410-G-T

Variant summary

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

The ENST00000655237.1(ENSG00000287463):n.389G>T 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 0.722 in 152,078 control chromosomes in the GnomAD database, including 42,255 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 0.72 (42255 hom., cov: 32)
• Consequence: ENST00000655237.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373629	XR_923354.4	n.465G>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000655237.1	n.389G>T		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109690 AN: 151960 Hom.: 42187 Cov.: 32

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.722 AC: 109819 AN: 152078 Hom.: 42255 Cov.: 32 AF XY: 0.731 AC XY: 54311 AN XY: 74318

Gnomad4 AFR AF: 0.918

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.911

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.887

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.791

Alfa AF: 0.633 Hom.: 42906

Bravo AF: 0.751

Asia WGS AF: 0.944 AC: 3282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.7
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6723108; hg19: chr2-135479980;