20-37678154-C-T

Variant names:

• chr20-37678154-C-T
• rs928199
• ENST00000373508.2:n.377C>T

Variant summary

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

The ENST00000373508.2(ENSG00000204117):​n.377C>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 0.0985 in 152,848 control chromosomes in the GnomAD database, including 1,030 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 0.099 (1030 hom., cov: 32)
  • Exomes 𝑓: 0.080 (0 hom.)
• Consequence: ENSG00000204117 ENST00000373508.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 3 publications found

Genes affected

ENSG00000204117 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000373508.2. 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
	LOC100287792	NR_040021.1		n.374C>T		non_coding_transcript_exon	Exon 2 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000204117	ENST00000373508.2	TSL:2	n.377C>T		non_coding_transcript_exon	Exon 2 of 4
	ENSG00000204117	ENST00000655861.1		n.199-186C>T		intron	N/A
	ENSG00000204117	ENST00000815582.1		n.202-186C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0986 AC: 15004 AN: 152158 Hom.: 1030 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.0747

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.0293

Gnomad SAS AF: 0.0325

Gnomad FIN AF: 0.0775

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.106

GnomAD4 exome AF: 0.0804 AC: 46 AN: 572 Hom.: 0 Cov.: 0 AF XY: 0.0773 AC XY: 28 AN XY: 362

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

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

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

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0810 AC: 35 AN: 432

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0727 AC: 8 AN: 110

Other (OTH) AF: 0.0500 AC: 1 AN: 20

GnomAD4 genome AF: 0.0986 AC: 15017 AN: 152276 Hom.: 1030 Cov.: 32 AF XY: 0.0978 AC XY: 7283 AN XY: 74456

African (AFR) AF: 0.188 AC: 7816 AN: 41530

American (AMR) AF: 0.0748 AC: 1145 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3472

East Asian (EAS) AF: 0.0293 AC: 152 AN: 5182

South Asian (SAS) AF: 0.0327 AC: 158 AN: 4832

European-Finnish (FIN) AF: 0.0775 AC: 822 AN: 10612

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0640 AC: 4355 AN: 68028

Other (OTH) AF: 0.104 AC: 220 AN: 2114

Alfa AF: 0.0880 Hom.: 118

Bravo AF: 0.103

Asia WGS AF: 0.0410 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.55
PhyloP100		-1.5

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: rs928199;

hg19: chr20-36306556;