rs1923508

chr1-152499244-C-A

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 0.138 in 152,120 control chromosomes in the GnomAD database, including 3,421 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 0.14 (3421 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 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: 0.138 AC: 21036 AN: 152002 Hom.: 3410 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0210

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0181

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.138 AC: 21065 AN: 152120 Hom.: 3421 Cov.: 32 AF XY: 0.138 AC XY: 10231 AN XY: 74388

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0210

Gnomad4 NFE AF: 0.0181

Gnomad4 OTH AF: 0.108

Alfa AF: 0.101 Hom.: 355

Bravo AF: 0.158

Asia WGS AF: 0.133 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.6
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1923508; hg19: chr1-152471720;