rs7529377

Variant names:

• chr1-173496185-G-A
• rs7529377

Your query was ambiguous. Multiple possible variants found:

• chr1-173496185-G-A
• chr1-173496185-G-T

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 0.211 in 152,040 control chromosomes in the GnomAD database, including 3,589 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 0.21 (3589 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 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: 0.211 AC: 32010 AN: 151922 Hom.: 3579 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.211 AC: 32068 AN: 152040 Hom.: 3589 Cov.: 32 AF XY: 0.209 AC XY: 15512 AN XY: 74306

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.209

Alfa AF: 0.0868 Hom.: 96

Bravo AF: 0.220

Asia WGS AF: 0.210 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7529377; hg19: chr1-173465324;