rs17561365

Variant names:

• chr10-36842573-C-A
• rs17561365

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 0.347 in 151,958 control chromosomes in the GnomAD database, including 9,300 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 0.35 (9300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 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: 0.347 AC: 52709 AN: 151840 Hom.: 9291 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.347 AC: 52736 AN: 151958 Hom.: 9300 Cov.: 32 AF XY: 0.342 AC XY: 25433 AN XY: 74274

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.330

Alfa AF: 0.370 Hom.: 1757

Bravo AF: 0.348

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	11
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17561365; hg19: chr10-37131501;