4-147361190-T-C

Variant names:

• chr4-147361190-T-C
• rs1429138

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 0.941 in 152,284 control chromosomes in the GnomAD database, including 67,453 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 0.94 (67453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.956 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: 0.941 AC: 143164 AN: 152166 Hom.: 67429 Cov.: 32

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.962

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.941 AC: 143243 AN: 152284 Hom.: 67453 Cov.: 32 AF XY: 0.940 AC XY: 69958 AN XY: 74456

African (AFR) AF: 0.924 AC: 38401 AN: 41542

American (AMR) AF: 0.931 AC: 14241 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.941 AC: 3266 AN: 3472

East Asian (EAS) AF: 0.812 AC: 4204 AN: 5180

South Asian (SAS) AF: 0.919 AC: 4433 AN: 4824

European-Finnish (FIN) AF: 0.955 AC: 10133 AN: 10610

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.962 AC: 65487 AN: 68042

Other (OTH) AF: 0.922 AC: 1945 AN: 2110

Alfa AF: 0.950 Hom.: 134335

Bravo AF: 0.937

Asia WGS AF: 0.858 AC: 2985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.53
DANN	Benign	0.55
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs1429138; hg19: chr4-148282342;