chr1-152499244-C-A

Variant names:

• chr1-152499244-C-A
• rs1923508

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 0.138 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.386 AC: 15992 AN: 41432

American (AMR) AF: 0.147 AC: 2245 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0133 AC: 46 AN: 3470

East Asian (EAS) AF: 0.100 AC: 518 AN: 5176

South Asian (SAS) AF: 0.108 AC: 519 AN: 4816

European-Finnish (FIN) AF: 0.0210 AC: 223 AN: 10600

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0181 AC: 1232 AN: 68026

Other (OTH) AF: 0.108 AC: 229 AN: 2114

Alfa AF: 0.110 Hom.: 422

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
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1923508; hg19: chr1-152471720;