rs6129005

Positions:

• chr20-61014216-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 0.321 in 152,014 control chromosomes in the GnomAD database, including 8,095 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 0.32 (8095 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48746 AN: 151896 Hom.: 8099 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.321 AC: 48759 AN: 152014 Hom.: 8095 Cov.: 32 AF XY: 0.325 AC XY: 24116 AN XY: 74296

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.338

Alfa AF: 0.341 Hom.: 18370

Bravo AF: 0.327

Asia WGS AF: 0.446 AC: 1549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.88
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6129005; hg19: chr20-59589272;