chr6-129760528-A-G

Variant names:

• chr6-129760528-A-G
• rs17057830

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 0.139 in 152,158 control chromosomes in the GnomAD database, including 1,710 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 0.14 (1710 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 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: 0.139 AC: 21135 AN: 152040 Hom.: 1700 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0681

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0824

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.139 AC: 21164 AN: 152158 Hom.: 1710 Cov.: 32 AF XY: 0.136 AC XY: 10091 AN XY: 74402

African (AFR) AF: 0.219 AC: 9085 AN: 41502

American (AMR) AF: 0.121 AC: 1847 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 385 AN: 3470

East Asian (EAS) AF: 0.0679 AC: 351 AN: 5170

South Asian (SAS) AF: 0.141 AC: 678 AN: 4822

European-Finnish (FIN) AF: 0.0824 AC: 875 AN: 10614

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7395 AN: 67986

Other (OTH) AF: 0.155 AC: 327 AN: 2110

Alfa AF: 0.121 Hom.: 1995

Bravo AF: 0.147

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.042
DANN	Benign	0.56
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs17057830; hg19: chr6-130081673;