rs9901283

Positions:

• chr17-74841693-G-A
• chr17-74841693-G-C

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 0.566 in 152,166 control chromosomes in the GnomAD database, including 25,160 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 0.57 (25160 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.629 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: 0.566 AC: 86130 AN: 152048 Hom.: 25154 Cov.: 34

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.566 AC: 86161 AN: 152166 Hom.: 25160 Cov.: 34 AF XY: 0.565 AC XY: 42062 AN XY: 74396

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.537

Alfa AF: 0.605 Hom.: 6207

Bravo AF: 0.557

Asia WGS AF: 0.411 AC: 1433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	18
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9901283; hg19: chr17-72837832;