rs6140362

chr20-7644859-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.157 in 152,152 control chromosomes in the GnomAD database, including 2,389 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 0.16 (2389 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

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: 0.157 AC: 23859 AN: 152034 Hom.: 2389 Cov.: 32

Gnomad AFR AF: 0.0463

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.157 AC: 23860 AN: 152152 Hom.: 2389 Cov.: 32 AF XY: 0.161 AC XY: 11944 AN XY: 74350

Gnomad4 AFR AF: 0.0461

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.0343

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.175

Alfa AF: 0.199 Hom.: 6490

Bravo AF: 0.144

Asia WGS AF: 0.0840 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.2
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6140362; hg19: chr20-7625506;