chr7-132028601-G-A

Variant names:

• chr7-132028601-G-A
• rs17166082

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.095 in 152,206 control chromosomes in the GnomAD database, including 1,145 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 0.095 (1145 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 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: 0.0949 AC: 14432 AN: 152088 Hom.: 1145 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0498

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.0643

Gnomad FIN AF: 0.0596

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0424

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0950 AC: 14457 AN: 152206 Hom.: 1145 Cov.: 32 AF XY: 0.0941 AC XY: 7002 AN XY: 74430

African (AFR) AF: 0.211 AC: 8750 AN: 41524

American (AMR) AF: 0.0498 AC: 761 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0213 AC: 74 AN: 3470

East Asian (EAS) AF: 0.157 AC: 811 AN: 5182

South Asian (SAS) AF: 0.0641 AC: 309 AN: 4818

European-Finnish (FIN) AF: 0.0596 AC: 631 AN: 10594

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0423 AC: 2879 AN: 68012

Other (OTH) AF: 0.0800 AC: 169 AN: 2112

Alfa AF: 0.0797 Hom.: 723

Bravo AF: 0.0985

Asia WGS AF: 0.125 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.65
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs17166082; hg19: chr7-131713360;