ENST00000564021.1:n.79C>A

Variant names:

• chr9-133633021-G-T
• rs1076153
• ENST00000564021.1:n.79C>A

Variant summary

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

The ENST00000564021.1(ENSG00000261018):​n.79C>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 0.235 in 152,226 control chromosomes in the GnomAD database, including 4,951 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 0.23 (4950 hom., cov: 32)
  • Exomes 𝑓: 0.14 (1 hom.)
• Consequence: ENSG00000261018 ENST00000564021.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 12 publications found

Genes affected

ENSG00000261018 (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 = 0.647 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000564021.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261018	ENST00000564021.1	TSL:3	n.79C>A		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35711 AN: 152028 Hom.: 4957 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.253

GnomAD4 exome AF: 0.138 AC: 11 AN: 80 Hom.: 1 Cov.: 0 AF XY: 0.161 AC XY: 9 AN XY: 56

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.167 AC: 2 AN: 12

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0962 AC: 5 AN: 52

Other (OTH) AF: 0.250 AC: 2 AN: 8

GnomAD4 genome AF: 0.235 AC: 35718 AN: 152146 Hom.: 4950 Cov.: 32 AF XY: 0.248 AC XY: 18447 AN XY: 74362

African (AFR) AF: 0.187 AC: 7768 AN: 41520

American (AMR) AF: 0.273 AC: 4171 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 950 AN: 3468

East Asian (EAS) AF: 0.666 AC: 3434 AN: 5158

South Asian (SAS) AF: 0.461 AC: 2220 AN: 4820

European-Finnish (FIN) AF: 0.287 AC: 3039 AN: 10584

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13289 AN: 67992

Other (OTH) AF: 0.252 AC: 531 AN: 2108

Alfa AF: 0.205 Hom.: 7710

Bravo AF: 0.231

Asia WGS AF: 0.523 AC: 1817 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	0.74
DANN	Benign	0.50
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1076153; hg19: chr9-136498143; COSMIC: COSV55040180;