rs469846

Variant names:

• chr1-91064032-G-A
• rs469846

Your query was ambiguous. Multiple possible variants found:

• chr1-91064032-G-A
• chr1-91064032-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 0.0771 in 152,192 control chromosomes in the GnomAD database, including 509 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 0.077 (509 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.148 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: 0.0769 AC: 11697 AN: 152074 Hom.: 503 Cov.: 32

Gnomad AFR AF: 0.0649

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.0614

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0788

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0682

Gnomad OTH AF: 0.0975

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

GnomAD4 genome AF: 0.0771 AC: 11731 AN: 152192 Hom.: 509 Cov.: 32 AF XY: 0.0792 AC XY: 5896 AN XY: 74402

African (AFR) AF: 0.0653 AC: 2710 AN: 41528

American (AMR) AF: 0.130 AC: 1984 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3466

East Asian (EAS) AF: 0.0614 AC: 317 AN: 5164

South Asian (SAS) AF: 0.158 AC: 760 AN: 4822

European-Finnish (FIN) AF: 0.0788 AC: 835 AN: 10594

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0681 AC: 4635 AN: 68012

Other (OTH) AF: 0.105 AC: 222 AN: 2114

Alfa AF: 0.0730 Hom.: 1020

Bravo AF: 0.0801

Asia WGS AF: 0.150 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.3
DANN	Benign	0.41
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs469846; hg19: chr1-91529589;