4-130044017-C-T

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 0.149 in 152,126 control chromosomes in the GnomAD database, including 4,540 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 0.15 (4540 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22558 AN: 152010 Hom.: 4525 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0906

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.0711

Gnomad SAS AF: 0.0460

Gnomad FIN AF: 0.0581

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.149 AC: 22620 AN: 152126 Hom.: 4540 Cov.: 32 AF XY: 0.146 AC XY: 10884 AN XY: 74368

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.0903

Gnomad4 ASJ AF: 0.00663

Gnomad4 EAS AF: 0.0714

Gnomad4 SAS AF: 0.0468

Gnomad4 FIN AF: 0.0581

Gnomad4 NFE AF: 0.0108

Gnomad4 OTH AF: 0.121

Alfa AF: 0.0142 Hom.: 36

Bravo AF: 0.164

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.7
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1395976; hg19: chr4-130965172;