ENST00000620690.1:n.262+61C>T

Variant names:

• chr1-160776286-G-A
• rs576523
• ENST00000792526.1:n.448C>T

Variant summary

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

The ENST00000620690.1(ENSG00000275801):​n.262+61C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.923 in 152,278 control chromosomes in the GnomAD database, including 65,859 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 0.92 (65831 hom., cov: 32)
  • Exomes 𝑓: 1.0 (28 hom.)
• Consequence: ENSG00000275801 ENST00000620690.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464
• Publications: 4 publications found

Genes affected

ENSG00000303180 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000620690.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105371470	NR_188635.1		n.398+33C>T		intron	N/A
	LOC105371470	NR_188636.1		n.398+33C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303180	ENST00000792526.1		n.448C>T		non_coding_transcript_exon	Exon 2 of 4
	ENSG00000303180	ENST00000792530.1		n.431C>T		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000275801	ENST00000620690.1	TSL:6	n.262+61C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.923 AC: 140401 AN: 152104 Hom.: 65808 Cov.: 32

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.967

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.997

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.942

GnomAD4 exome AF: 1.00 AC: 56 AN: 56 Hom.: 28 Cov.: 0 AF XY: 1.00 AC XY: 48 AN XY: 48

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 48 AN: 48

Other (OTH) AF: 1.00 AC: 4 AN: 4

GnomAD4 genome AF: 0.923 AC: 140475 AN: 152222 Hom.: 65831 Cov.: 32 AF XY: 0.925 AC XY: 68850 AN XY: 74428

African (AFR) AF: 0.737 AC: 30574 AN: 41468

American (AMR) AF: 0.968 AC: 14811 AN: 15308

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5176 AN: 5176

South Asian (SAS) AF: 0.997 AC: 4813 AN: 4826

European-Finnish (FIN) AF: 0.999 AC: 10622 AN: 10628

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.997 AC: 67838 AN: 68024

Other (OTH) AF: 0.942 AC: 1992 AN: 2114

Alfa AF: 0.980 Hom.: 121055

Bravo AF: 0.913

Asia WGS AF: 0.982 AC: 3416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.90
DANN	Benign	0.23
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs576523; hg19: chr1-160746076;