rs7524102

Variant names:

• chr1-22371954-A-G
• rs7524102

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 0.205 in 152,186 control chromosomes in the GnomAD database, including 3,671 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 (3671 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 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: 0.205 AC: 31172 AN: 152068 Hom.: 3665 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.0782

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.205 AC: 31208 AN: 152186 Hom.: 3671 Cov.: 32 AF XY: 0.199 AC XY: 14791 AN XY: 74416

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.0782

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.199

Alfa AF: 0.181 Hom.: 5731

Bravo AF: 0.216

Asia WGS AF: 0.217 AC: 756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.49
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7524102; hg19: chr1-22698447;