17-57246820-T-C

Variant names:

• chr17-57246820-T-C
• rs8073909

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 0.489 in 152,068 control chromosomes in the GnomAD database, including 19,781 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 0.49 (19781 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.699 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: 0.488 AC: 74216 AN: 151950 Hom.: 19733 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.410

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.489 AC: 74319 AN: 152068 Hom.: 19781 Cov.: 32 AF XY: 0.493 AC XY: 36608 AN XY: 74328

African (AFR) AF: 0.706 AC: 29256 AN: 41460

American (AMR) AF: 0.429 AC: 6561 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1570 AN: 3470

East Asian (EAS) AF: 0.601 AC: 3103 AN: 5164

South Asian (SAS) AF: 0.546 AC: 2627 AN: 4810

European-Finnish (FIN) AF: 0.399 AC: 4215 AN: 10570

Middle Eastern (MID) AF: 0.428 AC: 124 AN: 290

European-Non Finnish (NFE) AF: 0.376 AC: 25565 AN: 67988

Other (OTH) AF: 0.466 AC: 985 AN: 2114

Alfa AF: 0.413 Hom.: 7100

Bravo AF: 0.499

Asia WGS AF: 0.545 AC: 1898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.60
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs8073909; hg19: chr17-55324181;