4-145672445-A-G

Variant names:

• chr4-145672445-A-G
• rs950333

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 0.49 in 152,048 control chromosomes in the GnomAD database, including 19,329 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 0.49 (19329 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74385 AN: 151930 Hom.: 19301 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.490 AC: 74468 AN: 152048 Hom.: 19329 Cov.: 32 AF XY: 0.486 AC XY: 36143 AN XY: 74320

African (AFR) AF: 0.662 AC: 27465 AN: 41468

American (AMR) AF: 0.475 AC: 7270 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1713 AN: 3470

East Asian (EAS) AF: 0.569 AC: 2933 AN: 5158

South Asian (SAS) AF: 0.502 AC: 2422 AN: 4826

European-Finnish (FIN) AF: 0.299 AC: 3164 AN: 10574

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27832 AN: 67948

Other (OTH) AF: 0.514 AC: 1085 AN: 2110

Alfa AF: 0.425 Hom.: 6732

Bravo AF: 0.508

Asia WGS AF: 0.544 AC: 1894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.45
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs950333; hg19: chr4-146593597;