rs17154507

Positions:

• chr7-107836572-G-A

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.107836572G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;