17-36646020-A-C

Variant names:

• chr17-36646020-A-C
• rs3815053

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 0.357 in 152,064 control chromosomes in the GnomAD database, including 11,731 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 0.36 (11731 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54232 AN: 151946 Hom.: 11734 Cov.: 32

Gnomad AFR AF: 0.0927

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.357 AC: 54220 AN: 152064 Hom.: 11731 Cov.: 32 AF XY: 0.361 AC XY: 26800 AN XY: 74322

African (AFR) AF: 0.0925 AC: 3839 AN: 41504

American (AMR) AF: 0.377 AC: 5765 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1578 AN: 3468

East Asian (EAS) AF: 0.445 AC: 2293 AN: 5152

South Asian (SAS) AF: 0.411 AC: 1979 AN: 4820

European-Finnish (FIN) AF: 0.521 AC: 5490 AN: 10546

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31918 AN: 67982

Other (OTH) AF: 0.381 AC: 802 AN: 2106

Alfa AF: 0.448 Hom.: 8434

Bravo AF: 0.334

Asia WGS AF: 0.369 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	12
DANN	Benign	0.60
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs3815053; hg19: chr17-35002476;