rs17749681

Variant names:

• chr16-9713930-T-C
• rs17749681

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;