ENST00000630976.1:n.169C>T

Variant names:

• chr20-48471476-C-T
• rs6122689
• ENST00000630976.1:n.169C>T

Variant summary

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

The ENST00000630976.1(ENSG00000281365):​n.169C>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 0.195 in 152,212 control chromosomes in the GnomAD database, including 3,125 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 0.20 (3124 hom., cov: 32)
  • Exomes 𝑓: 0.12 (1 hom.)
• Consequence: ENSG00000281365 ENST00000630976.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 1 publications found

Genes affected

ENSG00000281365 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000630976.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000281365	ENST00000630976.1	TSL:2	n.169C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000281365	ENST00000788316.1		n.139C>T		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29662 AN: 151990 Hom.: 3121 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.0843

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.213

GnomAD4 exome AF: 0.123 AC: 13 AN: 106 Hom.: 1 Cov.: 0 AF XY: 0.147 AC XY: 10 AN XY: 68

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

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: 0.110 AC: 11 AN: 100

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.195 AC: 29680 AN: 152106 Hom.: 3124 Cov.: 32 AF XY: 0.192 AC XY: 14271 AN XY: 74364

African (AFR) AF: 0.243 AC: 10100 AN: 41482

American (AMR) AF: 0.172 AC: 2625 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3472

East Asian (EAS) AF: 0.259 AC: 1336 AN: 5164

South Asian (SAS) AF: 0.248 AC: 1193 AN: 4808

European-Finnish (FIN) AF: 0.0843 AC: 892 AN: 10578

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12124 AN: 67998

Other (OTH) AF: 0.209 AC: 442 AN: 2116

Alfa AF: 0.187 Hom.: 351

Bravo AF: 0.203

Asia WGS AF: 0.223 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.48
DANN	Benign	0.43
PhyloP100		-1.1

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: rs6122689;

hg19: chr20-47099722;