rs1321073

Variant names:

• chr1-11891569-G-A
• rs1321073

Your query was ambiguous. Multiple possible variants found:

• chr1-11891569-G-A
• chr1-11891569-G-C

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 0.441 in 151,878 control chromosomes in the GnomAD database, including 15,414 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 0.44 (15414 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208
• Publications: 7 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 (AFR) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66915 AN: 151760 Hom.: 15382 Cov.: 31

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.337

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.441 AC: 67016 AN: 151878 Hom.: 15414 Cov.: 31 AF XY: 0.446 AC XY: 33124 AN XY: 74226

African (AFR) AF: 0.545 AC: 22577 AN: 41412

American (AMR) AF: 0.386 AC: 5890 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1022 AN: 3470

East Asian (EAS) AF: 0.518 AC: 2670 AN: 5150

South Asian (SAS) AF: 0.464 AC: 2232 AN: 4810

European-Finnish (FIN) AF: 0.535 AC: 5631 AN: 10530

Middle Eastern (MID) AF: 0.362 AC: 105 AN: 290

European-Non Finnish (NFE) AF: 0.380 AC: 25812 AN: 67942

Other (OTH) AF: 0.422 AC: 887 AN: 2102

Alfa AF: 0.408 Hom.: 5546

Bravo AF: 0.431

Asia WGS AF: 0.500 AC: 1738 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	2.3
DANN	Benign	0.47
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1321073; hg19: chr1-11951626;