rs3761202

Positions:

• chr20-57106127-C-T

Variant summary

Our verdict is Benign. Variant got -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: ENST00000442780.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000442780.1	n.116C>T		non_coding_transcript_exon_variant	2/3	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

Gnomad4 AFR exome AF: 0.333

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.167

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

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.265

Alfa AF: 0.278 Hom.: 1439

Bravo AF: 0.299

Asia WGS AF: 0.345 AC: 1201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3761202; hg19: chr20-55681183;