4-73876266-C-T

Position:

• chr4-73876266-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 0.18 in 152,046 control chromosomes in the GnomAD database, including 2,849 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 0.18 (2849 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527

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 (AMR) allele frequency at 95% confidence interval = 0.316 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: 0.180 AC: 27315 AN: 151926 Hom.: 2837 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.180 AC: 27344 AN: 152046 Hom.: 2849 Cov.: 32 AF XY: 0.185 AC XY: 13725 AN XY: 74334

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.207

Alfa AF: 0.187 Hom.: 735

Bravo AF: 0.190

Asia WGS AF: 0.211 AC: 735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4422395; hg19: chr4-74741983;