rs723821

chr1-165047475-C-Achr1-165047475-C-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.180

Alfa AF: 0.131 Hom.: 4018

Bravo AF: 0.198

Asia WGS AF: 0.419 AC: 1455 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	6.3
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs723821; hg19: chr1-165016712;