4-145672445-A-G

Variant names:

• chr4-145672445-A-G
• rs950333

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 0.49 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.490 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

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.514

Alfa AF: 0.425 Hom.: 5995

Bravo AF: 0.508

Asia WGS AF: 0.544 AC: 1894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs950333; hg19: chr4-146593597;