rs6129005

Variant names:

• chr20-61014216-C-T
• rs6129005

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 0.321 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.249 AC: 10324 AN: 41494

American (AMR) AF: 0.385 AC: 5880 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1270 AN: 3468

East Asian (EAS) AF: 0.471 AC: 2428 AN: 5152

South Asian (SAS) AF: 0.495 AC: 2387 AN: 4818

European-Finnish (FIN) AF: 0.301 AC: 3171 AN: 10552

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22248 AN: 67954

Other (OTH) AF: 0.338 AC: 712 AN: 2108

Alfa AF: 0.335 Hom.: 27362

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
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs6129005; hg19: chr20-59589272;