chr1-165047475-C-A

Variant names:

• chr1-165047475-C-A
• rs723821

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 0.181 in 152,188 control chromosomes in the GnomAD database, including 3,326 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 0.18 (3326 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 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: 0.181 AC: 27504 AN: 152066 Hom.: 3327 Cov.: 33

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.181 AC: 27534 AN: 152188 Hom.: 3326 Cov.: 33 AF XY: 0.190 AC XY: 14132 AN XY: 74426

African (AFR) AF: 0.225 AC: 9330 AN: 41516

American (AMR) AF: 0.306 AC: 4674 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 409 AN: 3470

East Asian (EAS) AF: 0.480 AC: 2484 AN: 5170

South Asian (SAS) AF: 0.330 AC: 1593 AN: 4820

European-Finnish (FIN) AF: 0.157 AC: 1668 AN: 10598

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6927 AN: 68012

Other (OTH) AF: 0.180 AC: 381 AN: 2112

Alfa AF: 0.139 Hom.: 8665

Bravo AF: 0.198

Asia WGS AF: 0.419 AC: 1455 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.3
DANN	Benign	0.78
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs723821; hg19: chr1-165016712;