ENST00000566840.1:n.333G>A

Variant names:

• chr2-10021910-G-A
• rs4073397
• ENST00000566840.1:n.333G>A

Variant summary

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

The ENST00000566840.1(ENSG00000260476):​n.333G>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 0.343 in 152,058 control chromosomes in the GnomAD database, including 9,091 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 0.34 (9091 hom., cov: 32)
  • Exomes 𝑓: 0.21 (0 hom.)
• Consequence: ENSG00000260476 ENST00000566840.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 5 publications found

Genes affected

ENSG00000260476 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000566840.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260476	ENST00000566840.1	TSL:6	n.333G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000295440	ENST00000730125.1		n.544-1991G>A		intron	N/A
	ENSG00000295440	ENST00000730126.1		n.318-1991G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52154 AN: 151916 Hom.: 9077 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.319

GnomAD4 exome AF: 0.208 AC: 5 AN: 24 Hom.: 0 Cov.: 0 AF XY: 0.222 AC XY: 4 AN XY: 18

African (AFR) AC: 0 AN: 0

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) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.188 AC: 3 AN: 16

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.343 AC: 52188 AN: 152034 Hom.: 9091 Cov.: 32 AF XY: 0.342 AC XY: 25389 AN XY: 74318

African (AFR) AF: 0.347 AC: 14369 AN: 41468

American (AMR) AF: 0.329 AC: 5020 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 895 AN: 3460

East Asian (EAS) AF: 0.506 AC: 2615 AN: 5168

South Asian (SAS) AF: 0.408 AC: 1968 AN: 4826

European-Finnish (FIN) AF: 0.334 AC: 3518 AN: 10548

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22749 AN: 67972

Other (OTH) AF: 0.321 AC: 678 AN: 2114

Alfa AF: 0.336 Hom.: 37245

Bravo AF: 0.344

Asia WGS AF: 0.452 AC: 1570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.22
DANN	Benign	0.78
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4073397; hg19: chr2-10162037;