chr4-129333779-T-C

Position:

• chr4-129333779-T-C

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 0.0533 in 152,208 control chromosomes in the GnomAD database, including 615 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 0.053 (615 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.161 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: 0.0533 AC: 8099 AN: 152090 Hom.: 613 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0305

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.00985

Gnomad SAS AF: 0.0635

Gnomad FIN AF: 0.00339

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.00450

Gnomad OTH AF: 0.0449

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

GnomAD4 genome AF: 0.0533 AC: 8119 AN: 152208 Hom.: 615 Cov.: 32 AF XY: 0.0536 AC XY: 3992 AN XY: 74426

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.0304

Gnomad4 ASJ AF: 0.0104

Gnomad4 EAS AF: 0.00987

Gnomad4 SAS AF: 0.0635

Gnomad4 FIN AF: 0.00339

Gnomad4 NFE AF: 0.00448

Gnomad4 OTH AF: 0.0444

Alfa AF: 0.0362 Hom.: 56

Bravo AF: 0.0599

Asia WGS AF: 0.0550 AC: 192 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
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: rs10518547; hg19: chr4-130254934;