rs4845456

Variant names:

• chr1-152625924-G-A
• rs4845456

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 0.368 in 151,992 control chromosomes in the GnomAD database, including 10,337 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 0.37 (10337 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55936 AN: 151874 Hom.: 10323 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.368 AC: 55983 AN: 151992 Hom.: 10337 Cov.: 32 AF XY: 0.366 AC XY: 27178 AN XY: 74284

African (AFR) AF: 0.403 AC: 16697 AN: 41434

American (AMR) AF: 0.327 AC: 4993 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3464

East Asian (EAS) AF: 0.321 AC: 1654 AN: 5160

South Asian (SAS) AF: 0.287 AC: 1383 AN: 4822

European-Finnish (FIN) AF: 0.374 AC: 3956 AN: 10568

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25347 AN: 67950

Other (OTH) AF: 0.371 AC: 783 AN: 2110

Alfa AF: 0.371 Hom.: 1741

Bravo AF: 0.365

Asia WGS AF: 0.321 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.6
DANN	Benign	0.35
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4845456; hg19: chr1-152598400;