rs11582903

Positions:

• chr1-87380371-C-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 0.0776 in 151,936 control chromosomes in the GnomAD database, including 540 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 0.078 (540 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0776 AC: 11787 AN: 151818 Hom.: 538 Cov.: 32

Gnomad AFR AF: 0.0518

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0562

Gnomad ASJ AF: 0.0765

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.0822

Gnomad FIN AF: 0.0570

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0694

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

GnomAD4 genome AF: 0.0776 AC: 11794 AN: 151936 Hom.: 540 Cov.: 32 AF XY: 0.0744 AC XY: 5530 AN XY: 74304

Gnomad4 AFR AF: 0.0519

Gnomad4 AMR AF: 0.0562

Gnomad4 ASJ AF: 0.0765

Gnomad4 EAS AF: 0.00425

Gnomad4 SAS AF: 0.0821

Gnomad4 FIN AF: 0.0570

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0697

Alfa AF: 0.0830 Hom.: 80

Bravo AF: 0.0753

Asia WGS AF: 0.0490 AC: 169 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11582903; hg19: chr1-87846054;