chr1-212683643-C-G

Variant names:

• chr1-212683643-C-G
• rs2501856

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 0.415 in 152,032 control chromosomes in the GnomAD database, including 14,075 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 0.42 (14075 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 4 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 (AMR) allele frequency at 95% confidence interval = 0.539 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: 0.415 AC: 63108 AN: 151912 Hom.: 14053 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.415 AC: 63157 AN: 152032 Hom.: 14075 Cov.: 32 AF XY: 0.424 AC XY: 31483 AN XY: 74298

African (AFR) AF: 0.252 AC: 10459 AN: 41438

American (AMR) AF: 0.549 AC: 8390 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1742 AN: 3472

East Asian (EAS) AF: 0.500 AC: 2587 AN: 5170

South Asian (SAS) AF: 0.496 AC: 2394 AN: 4824

European-Finnish (FIN) AF: 0.525 AC: 5536 AN: 10554

Middle Eastern (MID) AF: 0.483 AC: 140 AN: 290

European-Non Finnish (NFE) AF: 0.448 AC: 30484 AN: 67988

Other (OTH) AF: 0.458 AC: 967 AN: 2112

Alfa AF: 0.276 Hom.: 676

Bravo AF: 0.413

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.069
DANN	Benign	0.37
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2501856; hg19: chr1-212856985;