rs17154507

Variant names:

• chr7-107836572-G-A
• rs17154507

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.146 in 152,094 control chromosomes in the GnomAD database, including 1,848 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 0.15 (1848 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.321 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: 0.146 AC: 22251 AN: 151976 Hom.: 1848 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.146 AC: 22253 AN: 152094 Hom.: 1848 Cov.: 32 AF XY: 0.147 AC XY: 10939 AN XY: 74324

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.178

Alfa AF: 0.149 Hom.: 1378

Bravo AF: 0.147

Asia WGS AF: 0.268 AC: 934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	9.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17154507; hg19: chr7-107477017;