rs17746916

Variant names:

• chr10-112945022-C-T
• rs17746916

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 0.0468 in 152,216 control chromosomes in the GnomAD database, including 223 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 0.047 (223 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0664 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: 0.0468 AC: 7118 AN: 152098 Hom.: 223 Cov.: 32

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0620

Gnomad ASJ AF: 0.0427

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.0501

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0681

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0468 AC: 7119 AN: 152216 Hom.: 223 Cov.: 32 AF XY: 0.0464 AC XY: 3449 AN XY: 74412

Gnomad4 AFR AF: 0.0120

Gnomad4 AMR AF: 0.0619

Gnomad4 ASJ AF: 0.0427

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0355

Gnomad4 FIN AF: 0.0501

Gnomad4 NFE AF: 0.0681

Gnomad4 OTH AF: 0.0601

Alfa AF: 0.0669 Hom.: 482

Bravo AF: 0.0450

Asia WGS AF: 0.0160 AC: 56 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.6
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17746916; hg19: chr10-114704781;