rs522807

Variant names:

• chr1-12164182-C-A
• rs522807

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 0.144 in 151,876 control chromosomes in the GnomAD database, including 3,591 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 0.14 (3591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.404 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: 0.144 AC: 21822 AN: 151758 Hom.: 3585 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.0668

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.0145

Gnomad SAS AF: 0.0257

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0458

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.144 AC: 21868 AN: 151876 Hom.: 3591 Cov.: 32 AF XY: 0.138 AC XY: 10248 AN XY: 74238

African (AFR) AF: 0.409 AC: 16898 AN: 41330

American (AMR) AF: 0.0667 AC: 1017 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 154 AN: 3468

East Asian (EAS) AF: 0.0146 AC: 75 AN: 5154

South Asian (SAS) AF: 0.0253 AC: 122 AN: 4818

European-Finnish (FIN) AF: 0.0164 AC: 173 AN: 10574

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0458 AC: 3111 AN: 67970

Other (OTH) AF: 0.125 AC: 264 AN: 2106

Alfa AF: 0.0735 Hom.: 2027

Bravo AF: 0.159

Asia WGS AF: 0.0500 AC: 174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.019
DANN	Benign	0.54
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs522807; hg19: chr1-12224239; COSMIC: COSV66163760;