ENST00000790561.1:n.62G>A

Variant names:

• chr20-58797137-C-T
• rs6100223
• ENST00000790561.1:n.62G>A

Variant summary

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

The ENST00000790561.1(ENSG00000302935):​n.62G>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 0.825 in 152,164 control chromosomes in the GnomAD database, including 52,409 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 0.83 (52409 hom., cov: 31)
• Consequence: ENSG00000302935 ENST00000790561.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 3 publications found

Genes affected

ENSG00000302935 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302935	ENST00000790561.1	n.62G>A		non_coding_transcript_exon_variant	Exon 2 of 5
ENSG00000302935	ENST00000790562.1	n.374G>A		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000302935	ENST00000790563.1	n.383G>A		non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125492 AN: 152046 Hom.: 52356 Cov.: 31

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.825 AC: 125603 AN: 152164 Hom.: 52409 Cov.: 31 AF XY: 0.823 AC XY: 61253 AN XY: 74382

African (AFR) AF: 0.957 AC: 39749 AN: 41518

American (AMR) AF: 0.742 AC: 11351 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2611 AN: 3472

East Asian (EAS) AF: 0.797 AC: 4108 AN: 5154

South Asian (SAS) AF: 0.824 AC: 3968 AN: 4816

European-Finnish (FIN) AF: 0.779 AC: 8253 AN: 10594

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.779 AC: 52945 AN: 68008

Other (OTH) AF: 0.801 AC: 1691 AN: 2112

Alfa AF: 0.804 Hom.: 7815

Bravo AF: 0.829

Asia WGS AF: 0.808 AC: 2813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.2
DANN	Benign	0.88
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6100223; hg19: chr20-57372192; COSMIC: COSV60105493;