rs11580380

Variant names:

• chr1-102194292-T-A
• rs11580380

Your query was ambiguous. Multiple possible variants found:

• chr1-102194292-T-A
• chr1-102194292-T-G

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 0.0821 in 152,188 control chromosomes in the GnomAD database, including 627 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 0.082 (627 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0822 AC: 12495 AN: 152068 Hom.: 627 Cov.: 32

Gnomad AFR AF: 0.0443

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0894

Gnomad OTH AF: 0.0554

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

GnomAD4 genome AF: 0.0821 AC: 12500 AN: 152188 Hom.: 627 Cov.: 32 AF XY: 0.0856 AC XY: 6365 AN XY: 74384

African (AFR) AF: 0.0443 AC: 1839 AN: 41558

American (AMR) AF: 0.108 AC: 1648 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0496 AC: 172 AN: 3468

East Asian (EAS) AF: 0.120 AC: 623 AN: 5176

South Asian (SAS) AF: 0.100 AC: 483 AN: 4820

European-Finnish (FIN) AF: 0.131 AC: 1384 AN: 10570

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0894 AC: 6078 AN: 68002

Other (OTH) AF: 0.0558 AC: 118 AN: 2116

Alfa AF: 0.0891 Hom.: 77

Bravo AF: 0.0782

Asia WGS AF: 0.125 AC: 434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.61
DANN	Benign	0.64
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs11580380; hg19: chr1-102659848;