rs17369334

chr10-15481068-T-G

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 0.0551 in 152,284 control chromosomes in the GnomAD database, including 265 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 0.055 (265 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0684 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: 0.0551 AC: 8380 AN: 152164 Hom.: 266 Cov.: 33

Gnomad AFR AF: 0.0704

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0372

Gnomad ASJ AF: 0.0426

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.0685

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0548

Gnomad OTH AF: 0.0473

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

GnomAD4 genome AF: 0.0551 AC: 8390 AN: 152284 Hom.: 265 Cov.: 33 AF XY: 0.0546 AC XY: 4068 AN XY: 74458

Gnomad4 AFR AF: 0.0705

Gnomad4 AMR AF: 0.0372

Gnomad4 ASJ AF: 0.0426

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0241

Gnomad4 FIN AF: 0.0685

Gnomad4 NFE AF: 0.0548

Gnomad4 OTH AF: 0.0468

Alfa AF: 0.0561 Hom.: 39

Bravo AF: 0.0536

Asia WGS AF: 0.0150 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	4.1
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17369334; hg19: chr10-15523067;