20-31510118-T-G

Variant names:

• chr20-31510118-T-G
• rs1205689

Variant summary

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

The variant allele was found at a frequency of 0.00895 in 151,856 control chromosomes in the GnomAD database, including 18 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 0.0089 (18 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00895 (1359/151856) while in subpopulation EAS AF = 0.0425 (219/5150). AF 95% confidence interval is 0.0379. There are 18 homozygotes in GnomAd4. There are 765 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 18 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

Frequencies

GnomAD3 genomes AF: 0.00892 AC: 1353 AN: 151736 Hom.: 17 Cov.: 32

Gnomad AFR AF: 0.00252

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0326

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.0428

Gnomad SAS AF: 0.00229

Gnomad FIN AF: 0.0141

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00512

Gnomad OTH AF: 0.00671

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00895 AC: 1359 AN: 151856 Hom.: 18 Cov.: 32 AF XY: 0.0103 AC XY: 765 AN XY: 74204

African (AFR) AF: 0.00251 AC: 104 AN: 41390

American (AMR) AF: 0.0331 AC: 504 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3472

East Asian (EAS) AF: 0.0425 AC: 219 AN: 5150

South Asian (SAS) AF: 0.00229 AC: 11 AN: 4804

European-Finnish (FIN) AF: 0.0141 AC: 148 AN: 10526

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.00512 AC: 348 AN: 67960

Other (OTH) AF: 0.00664 AC: 14 AN: 2108

Alfa AF: 0.00609 Hom.: 2

Bravo AF: 0.0103

Asia WGS AF: 0.0260 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.41
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs1205689; hg19: chr20-30097921;