4-147401235-A-G

Position:

• chr4-147401235-A-G

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 0.899 in 152,042 control chromosomes in the GnomAD database, including 61,977 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 0.90 (61977 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136557 AN: 151924 Hom.: 61943 Cov.: 31

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.982

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.961

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.899 AC: 136642 AN: 152042 Hom.: 61977 Cov.: 31 AF XY: 0.900 AC XY: 66884 AN XY: 74310

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.916

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 0.931

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.982

Gnomad4 NFE AF: 0.961

Gnomad4 OTH AF: 0.894

Alfa AF: 0.945 Hom.: 136776

Bravo AF: 0.888

Asia WGS AF: 0.890 AC: 3096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1429107; hg19: chr4-148322387;