chr4-119322567-T-C

Position:

• chr4-119322567-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 0.567 in 151,928 control chromosomes in the GnomAD database, including 24,447 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 0.57 (24447 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260

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 (EAS) allele frequency at 95% confidence interval = 0.61 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: 0.567 AC: 86052 AN: 151810 Hom.: 24414 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.567 AC: 86151 AN: 151928 Hom.: 24447 Cov.: 32 AF XY: 0.564 AC XY: 41879 AN XY: 74244

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.599

Alfa AF: 0.565 Hom.: 3633

Bravo AF: 0.579

Asia WGS AF: 0.635 AC: 2207 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	6.6
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: rs2282688; hg19: chr4-120243722;