6-129741572-T-C

Variant names:

• chr6-129741572-T-C
• rs208869

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 0.483 in 152,066 control chromosomes in the GnomAD database, including 17,864 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 0.48 (17864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.99
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.507 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: 0.483 AC: 73453 AN: 151946 Hom.: 17848 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.483 AC: 73518 AN: 152066 Hom.: 17864 Cov.: 32 AF XY: 0.483 AC XY: 35913 AN XY: 74340

African (AFR) AF: 0.505 AC: 20962 AN: 41474

American (AMR) AF: 0.501 AC: 7667 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1556 AN: 3470

East Asian (EAS) AF: 0.495 AC: 2557 AN: 5168

South Asian (SAS) AF: 0.524 AC: 2524 AN: 4814

European-Finnish (FIN) AF: 0.435 AC: 4592 AN: 10560

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32118 AN: 67978

Other (OTH) AF: 0.485 AC: 1024 AN: 2110

Alfa AF: 0.470 Hom.: 27587

Bravo AF: 0.486

Asia WGS AF: 0.496 AC: 1730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.065
DANN	Benign	0.40
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs208869; hg19: chr6-130062717;