rs6125345

Variant names:

• chr20-48491735-T-C
• rs6125345

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 0.168 in 151,968 control chromosomes in the GnomAD database, including 2,617 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 0.17 (2617 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.346 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: 0.168 AC: 25566 AN: 151850 Hom.: 2617 Cov.: 31

Gnomad AFR AF: 0.0761

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.168 AC: 25561 AN: 151968 Hom.: 2617 Cov.: 31 AF XY: 0.168 AC XY: 12472 AN XY: 74280

Gnomad4 AFR AF: 0.0759

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.189

Alfa AF: 0.207 Hom.: 6879

Bravo AF: 0.164

Asia WGS AF: 0.266 AC: 925 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	0.27
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6125345; hg19: chr20-47119981;