1-219632048-G-C

Variant names:

• chr1-219632048-G-C
• rs10495130

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 0.0789 in 152,116 control chromosomes in the GnomAD database, including 1,300 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 0.079 (1300 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 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: 0.0788 AC: 11970 AN: 151998 Hom.: 1296 Cov.: 33

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0447

Gnomad ASJ AF: 0.00806

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0891

Gnomad FIN AF: 0.00340

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0789 AC: 12001 AN: 152116 Hom.: 1300 Cov.: 33 AF XY: 0.0763 AC XY: 5677 AN XY: 74356

African (AFR) AF: 0.241 AC: 9975 AN: 41468

American (AMR) AF: 0.0444 AC: 679 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00806 AC: 28 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5168

South Asian (SAS) AF: 0.0894 AC: 431 AN: 4820

European-Finnish (FIN) AF: 0.00340 AC: 36 AN: 10586

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0102 AC: 692 AN: 67998

Other (OTH) AF: 0.0672 AC: 142 AN: 2114

Alfa AF: 0.0148 Hom.: 19

Bravo AF: 0.0890

Asia WGS AF: 0.0610 AC: 214 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.0030
DANN	Benign	0.68
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10495130; hg19: chr1-219805390;