rs1500540

Variant names:

• chr20-6868767-A-G
• rs1500540

Variant summary

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

The variant allele was found at a frequency of 0.024 in 152,378 control chromosomes in the GnomAD database, including 76 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 0.024 (76 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0546 is higher than 0.05.

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: 0.0239 AC: 3643 AN: 152260 Hom.: 75 Cov.: 33

Gnomad AFR AF: 0.00598

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0574

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.0304

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0304

Gnomad OTH AF: 0.0148

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

GnomAD4 genome AF: 0.0240 AC: 3651 AN: 152378 Hom.: 76 Cov.: 33 AF XY: 0.0240 AC XY: 1788 AN XY: 74514

African (AFR) AF: 0.00596 AC: 248 AN: 41592

American (AMR) AF: 0.0578 AC: 884 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00749 AC: 26 AN: 3470

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5190

South Asian (SAS) AF: 0.0120 AC: 58 AN: 4832

European-Finnish (FIN) AF: 0.0304 AC: 323 AN: 10624

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0304 AC: 2070 AN: 68042

Other (OTH) AF: 0.0147 AC: 31 AN: 2116

Alfa AF: 0.0301 Hom.: 120

Bravo AF: 0.0250

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.70
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1500540; hg19: chr20-6849414;