chr17-55740741-G-T

Variant names:

• chr17-55740741-G-T
• rs1160027

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 0.397 in 151,868 control chromosomes in the GnomAD database, including 16,544 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 0.40 (16544 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 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: 0.397 AC: 60231 AN: 151748 Hom.: 16495 Cov.: 31

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.397 AC: 60344 AN: 151868 Hom.: 16544 Cov.: 31 AF XY: 0.391 AC XY: 29041 AN XY: 74226

African (AFR) AF: 0.784 AC: 32388 AN: 41334

American (AMR) AF: 0.387 AC: 5917 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 831 AN: 3468

East Asian (EAS) AF: 0.218 AC: 1125 AN: 5166

South Asian (SAS) AF: 0.169 AC: 816 AN: 4818

European-Finnish (FIN) AF: 0.220 AC: 2318 AN: 10530

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.235 AC: 15972 AN: 67958

Other (OTH) AF: 0.362 AC: 766 AN: 2114

Alfa AF: 0.284 Hom.: 15087

Bravo AF: 0.432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.42
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1160027; hg19: chr17-53818102;