17-41483351-G-C

Variant names:

• chr17-41483351-G-C
• rs3809889

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 0.0596 in 152,122 control chromosomes in the GnomAD database, including 557 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 0.060 (557 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 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: 0.0596 AC: 9056 AN: 152004 Hom.: 553 Cov.: 31

Gnomad AFR AF: 0.0154

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0478

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0484

Gnomad OTH AF: 0.0714

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

GnomAD4 genome AF: 0.0596 AC: 9072 AN: 152122 Hom.: 557 Cov.: 31 AF XY: 0.0635 AC XY: 4726 AN XY: 74390

African (AFR) AF: 0.0154 AC: 637 AN: 41494

American (AMR) AF: 0.156 AC: 2391 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0403 AC: 140 AN: 3470

East Asian (EAS) AF: 0.220 AC: 1139 AN: 5184

South Asian (SAS) AF: 0.154 AC: 742 AN: 4820

European-Finnish (FIN) AF: 0.0478 AC: 506 AN: 10586

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0485 AC: 3294 AN: 67974

Other (OTH) AF: 0.0707 AC: 149 AN: 2108

Alfa AF: 0.0491 Hom.: 42

Bravo AF: 0.0696

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.069
DANN	Benign	0.55
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs3809889; hg19: chr17-39639603;