ENST00000373508.2:n.1107A>G

Variant names:

• chr20-37682226-A-G
• rs6095722
• ENST00000373508.2:n.1107A>G

Variant summary

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

The ENST00000373508.2(ENSG00000204117):​n.1107A>G 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 0.176 in 151,096 control chromosomes in the GnomAD database, including 4,749 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 0.18 (4748 hom., cov: 31)
  • Exomes 𝑓: 0.057 (1 hom.)
• Consequence: ENSG00000204117 ENST00000373508.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100287792	NR_040021.1	n.1104A>G		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000204117	ENST00000373508.2	n.1107A>G		non_coding_transcript_exon_variant	Exon 4 of 4	2
ENSG00000204117	ENST00000655861.1	n.*19A>G		downstream_gene_variant
ENSG00000204117	ENST00000815582.1	n.*19A>G		downstream_gene_variant
ENSG00000204117	ENST00000815583.1	n.*100A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26572 AN: 150704 Hom.: 4746 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0286

Gnomad EAS AF: 0.0290

Gnomad SAS AF: 0.0337

Gnomad FIN AF: 0.0796

Gnomad MID AF: 0.0974

Gnomad NFE AF: 0.0653

Gnomad OTH AF: 0.155

GnomAD4 exome AF: 0.0567 AC: 17 AN: 300 Hom.: 1 Cov.: 0 AF XY: 0.0750 AC XY: 12 AN XY: 160

African (AFR) AF: 0.500 AC: 4 AN: 8

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 6

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.0347 AC: 5 AN: 144

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

European-Non Finnish (NFE) AF: 0.0446 AC: 5 AN: 112

Other (OTH) AF: 0.136 AC: 3 AN: 22

GnomAD4 genome AF: 0.176 AC: 26611 AN: 150796 Hom.: 4748 Cov.: 31 AF XY: 0.172 AC XY: 12672 AN XY: 73572

African (AFR) AF: 0.458 AC: 18836 AN: 41102

American (AMR) AF: 0.102 AC: 1538 AN: 15138

Ashkenazi Jewish (ASJ) AF: 0.0286 AC: 99 AN: 3464

East Asian (EAS) AF: 0.0291 AC: 149 AN: 5126

South Asian (SAS) AF: 0.0337 AC: 160 AN: 4754

European-Finnish (FIN) AF: 0.0796 AC: 808 AN: 10154

Middle Eastern (MID) AF: 0.0909 AC: 26 AN: 286

European-Non Finnish (NFE) AF: 0.0654 AC: 4430 AN: 67782

Other (OTH) AF: 0.154 AC: 319 AN: 2078

Alfa AF: 0.137 Hom.: 656

Bravo AF: 0.190

Asia WGS AF: 0.0650 AC: 225 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	6.2
DANN	Benign	0.37
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs6095722; hg19: chr20-36310628;