17-65333647-A-G

Variant names:

• chr17-65333647-A-G
• rs985574

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 0.199 in 152,124 control chromosomes in the GnomAD database, including 5,135 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 0.20 (5135 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 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: 0.199 AC: 30232 AN: 152006 Hom.: 5109 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0822

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0923

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.199 AC: 30318 AN: 152124 Hom.: 5135 Cov.: 32 AF XY: 0.195 AC XY: 14517 AN XY: 74388

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0536

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.0825

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0923

Gnomad4 OTH AF: 0.176

Alfa AF: 0.115 Hom.: 1951

Bravo AF: 0.213

Asia WGS AF: 0.118 AC: 412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.8
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs985574; hg19: chr17-63329765;