rs17749681

chr16-9713930-T-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 0.412 in 151,928 control chromosomes in the GnomAD database, including 13,069 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 0.41 (13069 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.544 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: 0.412 AC: 62528 AN: 151810 Hom.: 13057 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.412 AC: 62577 AN: 151928 Hom.: 13069 Cov.: 31 AF XY: 0.415 AC XY: 30815 AN XY: 74260

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.449

Alfa AF: 0.422 Hom.: 8161

Bravo AF: 0.406

Asia WGS AF: 0.518 AC: 1801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.44
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17749681; hg19: chr16-9807787;