chr1-152619708-C-T

Variant names:

• chr1-152619708-C-T
• rs4845454

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 0.58 in 151,930 control chromosomes in the GnomAD database, including 26,238 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 0.58 (26238 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.64 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: 0.580 AC: 88032 AN: 151812 Hom.: 26231 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.580 AC: 88073 AN: 151930 Hom.: 26238 Cov.: 32 AF XY: 0.585 AC XY: 43402 AN XY: 74252

African (AFR) AF: 0.422 AC: 17479 AN: 41428

American (AMR) AF: 0.623 AC: 9510 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2159 AN: 3468

East Asian (EAS) AF: 0.613 AC: 3154 AN: 5142

South Asian (SAS) AF: 0.632 AC: 3041 AN: 4814

European-Finnish (FIN) AF: 0.662 AC: 6987 AN: 10554

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.645 AC: 43812 AN: 67934

Other (OTH) AF: 0.581 AC: 1228 AN: 2112

Alfa AF: 0.616 Hom.: 46953

Bravo AF: 0.567

Asia WGS AF: 0.582 AC: 2025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.69
DANN	Benign	0.50
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4845454; hg19: chr1-152592184;