4-147401235-A-G

Variant names:

• chr4-147401235-A-G
• rs1429107

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 0.899 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.764 AC: 31650 AN: 41450

American (AMR) AF: 0.916 AC: 13982 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.925 AC: 3207 AN: 3468

East Asian (EAS) AF: 0.931 AC: 4811 AN: 5166

South Asian (SAS) AF: 0.882 AC: 4243 AN: 4808

European-Finnish (FIN) AF: 0.982 AC: 10418 AN: 10612

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.961 AC: 65306 AN: 67964

Other (OTH) AF: 0.894 AC: 1889 AN: 2112

Alfa AF: 0.938 Hom.: 286789

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
PhyloP100		-0.085

Splicing

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

Other links and lift over

dbSNP: rs1429107; hg19: chr4-148322387;