rs7545402

Variant names:

• chr1-100855520-G-A
• rs7545402

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 0.113 in 151,978 control chromosomes in the GnomAD database, including 1,225 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 0.11 (1225 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 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: 0.114 AC: 17237 AN: 151860 Hom.: 1225 Cov.: 32

Gnomad AFR AF: 0.0354

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0727

Gnomad SAS AF: 0.0500

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.113 AC: 17234 AN: 151978 Hom.: 1225 Cov.: 32 AF XY: 0.111 AC XY: 8265 AN XY: 74286

Gnomad4 AFR AF: 0.0353

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.0730

Gnomad4 SAS AF: 0.0500

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.123

Alfa AF: 0.141 Hom.: 225

Bravo AF: 0.108

Asia WGS AF: 0.0580 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7545402; hg19: chr1-101321076; COSMIC: COSV59978865;