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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.441 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

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.422

Alfa AF: 0.409 Hom.: 4605

Bravo AF: 0.431

Asia WGS AF: 0.500 AC: 1738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1321073; hg19: chr1-11951626;