rs11582903

Variant names:

• chr1-87380371-C-A
• rs11582903

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 0.0776 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0519 AC: 2151 AN: 41454

American (AMR) AF: 0.0562 AC: 857 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0765 AC: 265 AN: 3466

East Asian (EAS) AF: 0.00425 AC: 22 AN: 5178

South Asian (SAS) AF: 0.0821 AC: 396 AN: 4824

European-Finnish (FIN) AF: 0.0570 AC: 599 AN: 10500

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7238 AN: 67938

Other (OTH) AF: 0.0697 AC: 147 AN: 2110

Alfa AF: 0.0755 Hom.: 197

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
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs11582903; hg19: chr1-87846054;