20-37096280-T-G

Variant names:

• chr20-37096280-T-G
• rs1780703
• ENST00000598590.2:n.531T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000598590.2(ENSG00000269846):​n.531T>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 0.0103 in 187,200 control chromosomes in the GnomAD database, including 38 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 0.012 (35 hom., cov: 32)
  • Exomes 𝑓: 0.0018 (3 hom.)
• Consequence: ENSG00000269846 ENST00000598590.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.762
• Publications: 2 publications found

Genes affected

ENSG00000269846 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0122 (1863/152166) while in subpopulation AFR AF = 0.0421 (1747/41526). AF 95% confidence interval is 0.0404. There are 35 homozygotes in GnomAd4. There are 879 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 35 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000269846	ENST00000598590.2	n.531T>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000269846	ENST00000733134.1	n.251T>G		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0122 AC: 1861 AN: 152048 Hom.: 35 Cov.: 32

Gnomad AFR AF: 0.0421

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00682

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00574

GnomAD4 exome AF: 0.00183 AC: 64 AN: 35034 Hom.: 3 Cov.: 0 AF XY: 0.00151 AC XY: 27 AN XY: 17848

African (AFR) AF: 0.0372 AC: 55 AN: 1480

American (AMR) AF: 0.00260 AC: 3 AN: 1154

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1666

East Asian (EAS) AF: 0.00 AC: 0 AN: 2616

South Asian (SAS) AF: 0.00 AC: 0 AN: 772

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1724

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 198

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 22882

Other (OTH) AF: 0.00236 AC: 6 AN: 2542

GnomAD4 genome AF: 0.0122 AC: 1863 AN: 152166 Hom.: 35 Cov.: 32 AF XY: 0.0118 AC XY: 879 AN XY: 74390

African (AFR) AF: 0.0421 AC: 1747 AN: 41526

American (AMR) AF: 0.00681 AC: 104 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5150

South Asian (SAS) AF: 0.00 AC: 0 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10612

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67998

Other (OTH) AF: 0.00568 AC: 12 AN: 2112

Alfa AF: 0.0109 Hom.: 4

Bravo AF: 0.0139

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.1
DANN	Benign	0.54
PhyloP100		-0.76
PromoterAI		0.27	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1780703; hg19: chr20-35724683;