17-13604552-C-T

Variant names:

• chr17-13604552-C-T
• rs8074072

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 0.396 in 151,902 control chromosomes in the GnomAD database, including 15,207 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 (15207 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 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: 0.396 AC: 60038 AN: 151784 Hom.: 15164 Cov.: 32

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.396 AC: 60139 AN: 151902 Hom.: 15207 Cov.: 32 AF XY: 0.388 AC XY: 28770 AN XY: 74226

African (AFR) AF: 0.729 AC: 30212 AN: 41426

American (AMR) AF: 0.240 AC: 3658 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 938 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1097 AN: 5140

South Asian (SAS) AF: 0.323 AC: 1552 AN: 4808

European-Finnish (FIN) AF: 0.236 AC: 2488 AN: 10534

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19104 AN: 67954

Other (OTH) AF: 0.352 AC: 739 AN: 2102

Alfa AF: 0.314 Hom.: 4903

Bravo AF: 0.408

Asia WGS AF: 0.327 AC: 1136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.0
DANN	Benign	0.84
PhyloP100		-0.045

Splicing

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

Other links and lift over

dbSNP: rs8074072; hg19: chr17-13507869;