rs7583085

chr2-42795828-G-Achr2-42795828-G-T

Variant summary

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

The ENST00000692682.1(ENSG00000289082):n.503G>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 0.797 in 152,186 control chromosomes in the GnomAD database, including 48,752 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 0.80 (48752 hom., cov: 33)
• Consequence: ENST00000692682.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.894 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
	ENST00000692682.1	n.503G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.797 AC: 121268 AN: 152068 Hom.: 48714 Cov.: 33

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.797 AC: 121365 AN: 152186 Hom.: 48752 Cov.: 33 AF XY: 0.798 AC XY: 59356 AN XY: 74386

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.814

Alfa AF: 0.741 Hom.: 4407

Bravo AF: 0.809

Asia WGS AF: 0.878 AC: 3052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.4
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7583085; hg19: chr2-43022968;