rs7524102

Variant names:

• chr1-22371954-A-G
• rs7524102

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 0.205 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
• Publications: 74 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.312 AC: 12958 AN: 41502

American (AMR) AF: 0.146 AC: 2239 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 707 AN: 3468

East Asian (EAS) AF: 0.217 AC: 1119 AN: 5164

South Asian (SAS) AF: 0.218 AC: 1052 AN: 4826

European-Finnish (FIN) AF: 0.0782 AC: 830 AN: 10614

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11665 AN: 67990

Other (OTH) AF: 0.199 AC: 420 AN: 2114

Alfa AF: 0.183 Hom.: 11700

Bravo AF: 0.216

Asia WGS AF: 0.217 AC: 756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.49
DANN	Benign	0.38
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs7524102; hg19: chr1-22698447;