rs17057773

Positions:

• chr6-129749171-G-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 0.0865 in 152,210 control chromosomes in the GnomAD database, including 766 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 0.086 (766 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.129749171G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0864 AC: 13145 AN: 152092 Hom.: 767 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0653

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0364

Gnomad SAS AF: 0.0574

Gnomad FIN AF: 0.0304

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0561

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0865 AC: 13163 AN: 152210 Hom.: 766 Cov.: 32 AF XY: 0.0846 AC XY: 6297 AN XY: 74424

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.0652

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.0365

Gnomad4 SAS AF: 0.0574

Gnomad4 FIN AF: 0.0304

Gnomad4 NFE AF: 0.0561

Gnomad4 OTH AF: 0.0998

Alfa AF: 0.0667 Hom.: 292

Bravo AF: 0.0941

Asia WGS AF: 0.0550 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.31
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17057773; hg19: chr6-130070316;