chr1-229669248-C-G

Variant names:

• chr1-229669248-C-G
• rs10495285

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 0.254 in 152,182 control chromosomes in the GnomAD database, including 5,852 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 0.25 (5852 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38577 AN: 152064 Hom.: 5849 Cov.: 33

Gnomad AFR AF: 0.0980

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.0714

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.254 AC: 38580 AN: 152182 Hom.: 5852 Cov.: 33 AF XY: 0.250 AC XY: 18619 AN XY: 74408

African (AFR) AF: 0.0978 AC: 4061 AN: 41542

American (AMR) AF: 0.263 AC: 4026 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1282 AN: 3470

East Asian (EAS) AF: 0.0710 AC: 368 AN: 5186

South Asian (SAS) AF: 0.303 AC: 1462 AN: 4822

European-Finnish (FIN) AF: 0.322 AC: 3408 AN: 10574

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23071 AN: 67986

Other (OTH) AF: 0.268 AC: 566 AN: 2110

Alfa AF: 0.194 Hom.: 519

Bravo AF: 0.242

Asia WGS AF: 0.184 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.38
DANN	Benign	0.35
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs10495285; hg19: chr1-229804995;