rs411602

Variant names:

• chr17-70543436-C-T
• rs411602

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.305 in 151,982 control chromosomes in the GnomAD database, including 7,735 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 0.31 (7735 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.384 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: 0.305 AC: 46386 AN: 151864 Hom.: 7728 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.305 AC: 46392 AN: 151982 Hom.: 7735 Cov.: 31 AF XY: 0.297 AC XY: 22091 AN XY: 74282

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.338

Alfa AF: 0.359 Hom.: 2469

Bravo AF: 0.304

Asia WGS AF: 0.276 AC: 963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs411602; hg19: chr17-68539577;