ENST00000442780.1:n.116C>T

Variant names:

• chr20-57106127-C-T
• rs3761202
• ENST00000442780.1:n.116C>T

Variant summary

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

The ENST00000442780.1(ENSG00000231078):​n.116C>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 0.3 in 152,086 control chromosomes in the GnomAD database, including 7,145 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 0.30 (7145 hom., cov: 33)
  • Exomes 𝑓: 0.26 (0 hom.)
• Consequence: ENSG00000231078 ENST00000442780.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 1 publications found

Genes affected

ENSG00000231078 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000442780.1. 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
	ENSG00000231078	ENST00000442780.1	TSL:3	n.116C>T		non_coding_transcript_exon	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45541 AN: 151934 Hom.: 7140 Cov.: 33

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.265

GnomAD4 exome AF: 0.265 AC: 9 AN: 34 Hom.: 0 Cov.: 0 AF XY: 0.208 AC XY: 5 AN XY: 24

African (AFR) AF: 0.333 AC: 2 AN: 6

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) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.250 AC: 5 AN: 20

Other (OTH) AF: 0.167 AC: 1 AN: 6

GnomAD4 genome AF: 0.300 AC: 45594 AN: 152052 Hom.: 7145 Cov.: 33 AF XY: 0.302 AC XY: 22480 AN XY: 74328

African (AFR) AF: 0.376 AC: 15586 AN: 41480

American (AMR) AF: 0.323 AC: 4937 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3472

East Asian (EAS) AF: 0.261 AC: 1346 AN: 5166

South Asian (SAS) AF: 0.384 AC: 1851 AN: 4816

European-Finnish (FIN) AF: 0.292 AC: 3085 AN: 10566

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17199 AN: 67968

Other (OTH) AF: 0.265 AC: 561 AN: 2114

Alfa AF: 0.277 Hom.: 2342

Bravo AF: 0.299

Asia WGS AF: 0.345 AC: 1201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.76
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs3761202; hg19: chr20-55681183;