1-218447405-T-C

Variant names:

• chr1-218447405-T-C
• rs1473526

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 0.331 in 152,000 control chromosomes in the GnomAD database, including 9,084 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 0.33 (9084 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.31
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50289 AN: 151884 Hom.: 9072 Cov.: 31

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.331 AC: 50337 AN: 152000 Hom.: 9084 Cov.: 31 AF XY: 0.338 AC XY: 25074 AN XY: 74290

African (AFR) AF: 0.351 AC: 14550 AN: 41454

American (AMR) AF: 0.446 AC: 6802 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1067 AN: 3472

East Asian (EAS) AF: 0.704 AC: 3627 AN: 5154

South Asian (SAS) AF: 0.349 AC: 1677 AN: 4800

European-Finnish (FIN) AF: 0.306 AC: 3232 AN: 10560

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18265 AN: 67984

Other (OTH) AF: 0.336 AC: 709 AN: 2110

Alfa AF: 0.295 Hom.: 23882

Bravo AF: 0.347

Asia WGS AF: 0.468 AC: 1626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	17
DANN	Benign	0.67
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs1473526; hg19: chr1-218620747;