ENST00000823933.1:n.532C>T

Variant names:

• chr17-78342606-C-T
• rs4447485
• ENST00000823933.1:n.532C>T

Variant summary

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

The ENST00000823933.1(ENSG00000267737):​n.532C>T 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 0.149 in 152,424 control chromosomes in the GnomAD database, including 1,802 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 0.15 (1800 hom., cov: 32)
  • Exomes 𝑓: 0.13 (2 hom.)
• Consequence: ENSG00000267737 ENST00000823933.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390
• Publications: 7 publications found

Genes affected

ENSG00000267737 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000823933.1. 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
	LOC105371912	NR_188633.1		n.540C>T		non_coding_transcript_exon	Exon 1 of 2
	LOC105371912	NR_188632.1		n.74-1359C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267737	ENST00000823933.1		n.532C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000267737	ENST00000586321.1	TSL:3	n.61-1359C>T		intron	N/A
	ENSG00000267737	ENST00000823930.1		n.39-1359C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22691 AN: 152064 Hom.: 1802 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.0929

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.170

GnomAD4 exome AF: 0.128 AC: 31 AN: 242 Hom.: 2 AF XY: 0.139 AC XY: 25 AN XY: 180

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

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 20

European-Finnish (FIN) AF: 0.200 AC: 4 AN: 20

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

European-Non Finnish (NFE) AF: 0.137 AC: 25 AN: 182

Other (OTH) AF: 0.00 AC: 0 AN: 8

GnomAD4 genome AF: 0.149 AC: 22688 AN: 152182 Hom.: 1800 Cov.: 32 AF XY: 0.148 AC XY: 11044 AN XY: 74394

African (AFR) AF: 0.132 AC: 5479 AN: 41522

American (AMR) AF: 0.126 AC: 1931 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 882 AN: 3472

East Asian (EAS) AF: 0.0929 AC: 479 AN: 5156

South Asian (SAS) AF: 0.150 AC: 723 AN: 4830

European-Finnish (FIN) AF: 0.135 AC: 1436 AN: 10608

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11043 AN: 67974

Other (OTH) AF: 0.169 AC: 358 AN: 2114

Alfa AF: 0.161 Hom.: 3280

Bravo AF: 0.148

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.1
DANN	Benign	0.88
PhyloP100		0.39

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4447485;

hg19: chr17-76338687;