rs17154507

Variant names:

• chr7-107836572-G-A
• rs17154507

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.108 AC: 4464 AN: 41494

American (AMR) AF: 0.146 AC: 2234 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3470

East Asian (EAS) AF: 0.334 AC: 1728 AN: 5166

South Asian (SAS) AF: 0.223 AC: 1075 AN: 4814

European-Finnish (FIN) AF: 0.120 AC: 1271 AN: 10548

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10336 AN: 68002

Other (OTH) AF: 0.178 AC: 375 AN: 2112

Alfa AF: 0.151 Hom.: 2337

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
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs17154507; hg19: chr7-107477017;