rs1205689

chr20-31510118-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 17 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00251

Gnomad4 AMR AF: 0.0331

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.0425

Gnomad4 SAS AF: 0.00229

Gnomad4 FIN AF: 0.0141

Gnomad4 NFE AF: 0.00512

Gnomad4 OTH AF: 0.00664

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1205689; hg19: chr20-30097921;