rs7527580

chr1-19052014-G-A

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 0.0346 in 152,114 control chromosomes in the GnomAD database, including 144 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 0.035 (144 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0347 AC: 5267 AN: 151996 Hom.: 145 Cov.: 31

Gnomad AFR AF: 0.00855

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0304

Gnomad ASJ AF: 0.00865

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.0544

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0428

Gnomad OTH AF: 0.0235

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

GnomAD4 genome AF: 0.0346 AC: 5264 AN: 152114 Hom.: 144 Cov.: 31 AF XY: 0.0348 AC XY: 2587 AN XY: 74346

Gnomad4 AFR AF: 0.00853

Gnomad4 AMR AF: 0.0304

Gnomad4 ASJ AF: 0.00865

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.0643

Gnomad4 FIN AF: 0.0544

Gnomad4 NFE AF: 0.0428

Gnomad4 OTH AF: 0.0237

Alfa AF: 0.0392 Hom.: 186

Bravo AF: 0.0322

Asia WGS AF: 0.0830 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.039
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7527580; hg19: chr1-19378508;