rs17561365

chr10-36842573-C-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;