rs17057773

Variant names:

• chr6-129749171-G-T
• rs17057773

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 0.0865 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.166 AC: 6886 AN: 41524

American (AMR) AF: 0.0652 AC: 997 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3468

East Asian (EAS) AF: 0.0365 AC: 189 AN: 5182

South Asian (SAS) AF: 0.0574 AC: 277 AN: 4822

European-Finnish (FIN) AF: 0.0304 AC: 322 AN: 10596

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.0561 AC: 3818 AN: 68020

Other (OTH) AF: 0.0998 AC: 211 AN: 2114

Alfa AF: 0.0685 Hom.: 383

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs17057773; hg19: chr6-130070316;