rs11578508

chr1-207955720-A-G

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 0.285 in 152,148 control chromosomes in the GnomAD database, including 6,668 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 0.29 (6668 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.74

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 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: 0.286 AC: 43408 AN: 152030 Hom.: 6666 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.0389

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.285 AC: 43422 AN: 152148 Hom.: 6668 Cov.: 33 AF XY: 0.276 AC XY: 20520 AN XY: 74396

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.0390

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.288

Alfa AF: 0.295 Hom.: 1201

Bravo AF: 0.285

Asia WGS AF: 0.113 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.038
Dann	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11578508; hg19: chr1-208129065;