rs212306

Variant names:

• chr1-29392963-G-A
• rs212306

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 0.517 in 152,172 control chromosomes in the GnomAD database, including 20,991 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 0.52 (20991 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 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: 0.517 AC: 78568 AN: 152054 Hom.: 20989 Cov.: 34

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.517 AC: 78602 AN: 152172 Hom.: 20991 Cov.: 34 AF XY: 0.522 AC XY: 38810 AN XY: 74380

African (AFR) AF: 0.395 AC: 16387 AN: 41518

American (AMR) AF: 0.558 AC: 8538 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1907 AN: 3472

East Asian (EAS) AF: 0.658 AC: 3413 AN: 5184

South Asian (SAS) AF: 0.605 AC: 2916 AN: 4822

European-Finnish (FIN) AF: 0.582 AC: 6159 AN: 10586

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37402 AN: 67982

Other (OTH) AF: 0.557 AC: 1176 AN: 2110

Alfa AF: 0.544 Hom.: 90206

Bravo AF: 0.512

Asia WGS AF: 0.600 AC: 2084 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.64
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs212306; hg19: chr1-29719475; COSMIC: COSV59933334;