17-13159478-G-A

Position:

• chr17-13159478-G-A

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 0.0547 in 152,222 control chromosomes in the GnomAD database, including 308 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 (308 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0997 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0546 AC: 8308 AN: 152104 Hom.: 306 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0374

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.0596

Gnomad SAS AF: 0.0363

Gnomad FIN AF: 0.00754

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0387

Gnomad OTH AF: 0.0544

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

GnomAD4 genome AF: 0.0547 AC: 8329 AN: 152222 Hom.: 308 Cov.: 32 AF XY: 0.0531 AC XY: 3954 AN XY: 74422

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.0374

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.0597

Gnomad4 SAS AF: 0.0361

Gnomad4 FIN AF: 0.00754

Gnomad4 NFE AF: 0.0387

Gnomad4 OTH AF: 0.0539

Alfa AF: 0.0449 Hom.: 315

Bravo AF: 0.0596

Asia WGS AF: 0.0640 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.74
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9900808; hg19: chr17-13062795;