rs17320971

Variant names:

• chr17-42394899-A-G
• rs17320971

Your query was ambiguous. Multiple possible variants found:

• chr17-42394899-A-G
• chr17-42394899-A-T

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 0.0632 in 152,130 control chromosomes in the GnomAD database, including 352 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 0.063 (352 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

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 (NFE) allele frequency at 95% confidence interval = 0.0736 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: 0.0631 AC: 9589 AN: 152012 Hom.: 346 Cov.: 32

Gnomad AFR AF: 0.0430

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.0489

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.0705

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0753

Gnomad OTH AF: 0.0549

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

GnomAD4 genome AF: 0.0632 AC: 9620 AN: 152130 Hom.: 352 Cov.: 32 AF XY: 0.0636 AC XY: 4731 AN XY: 74364

Gnomad4 AFR AF: 0.0432

Gnomad4 AMR AF: 0.0488

Gnomad4 ASJ AF: 0.0441

Gnomad4 EAS AF: 0.0164

Gnomad4 SAS AF: 0.0706

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.0753

Gnomad4 OTH AF: 0.0614

Alfa AF: 0.0534 Hom.: 79

Bravo AF: 0.0563

Asia WGS AF: 0.0820 AC: 285 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	1.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17320971; hg19: chr17-40546917;