rs17315854

Variant names:

• chr7-86024657-T-C
• rs17315854

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 0.0961 in 151,940 control chromosomes in the GnomAD database, including 805 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 0.096 (805 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 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: 0.0961 AC: 14593 AN: 151822 Hom.: 804 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0447

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0732

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

GnomAD4 genome AF: 0.0961 AC: 14604 AN: 151940 Hom.: 805 Cov.: 32 AF XY: 0.0952 AC XY: 7069 AN XY: 74276

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.0446

Gnomad4 ASJ AF: 0.0680

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0244

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0724

Alfa AF: 0.0945 Hom.: 1012

Bravo AF: 0.0892

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17315854; hg19: chr7-85653973;