6-129716860-T-C

Variant names:

• chr6-129716860-T-C
• rs1984408

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 0.278 in 152,042 control chromosomes in the GnomAD database, including 6,117 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 0.28 (6117 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.359 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: 0.278 AC: 42287 AN: 151924 Hom.: 6108 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.0944

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.278 AC: 42333 AN: 152042 Hom.: 6117 Cov.: 32 AF XY: 0.276 AC XY: 20486 AN XY: 74342

African (AFR) AF: 0.291 AC: 12054 AN: 41448

American (AMR) AF: 0.315 AC: 4821 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 910 AN: 3466

East Asian (EAS) AF: 0.0944 AC: 490 AN: 5188

South Asian (SAS) AF: 0.374 AC: 1801 AN: 4820

European-Finnish (FIN) AF: 0.209 AC: 2207 AN: 10550

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19194 AN: 67972

Other (OTH) AF: 0.283 AC: 596 AN: 2104

Alfa AF: 0.287 Hom.: 9891

Bravo AF: 0.283

Asia WGS AF: 0.259 AC: 904 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	0.51
DANN	Benign	0.47
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1984408; hg19: chr6-130038005;