4-81263080-A-G

Variant names:

• chr4-81263080-A-G
• rs1878528

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 0.381 in 152,062 control chromosomes in the GnomAD database, including 12,130 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 0.38 (12130 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204

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 = 0.55 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: 0.381 AC: 57925 AN: 151946 Hom.: 12114 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.381 AC: 57988 AN: 152062 Hom.: 12130 Cov.: 32 AF XY: 0.378 AC XY: 28093 AN XY: 74332

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.333

Alfa AF: 0.332 Hom.: 8831

Bravo AF: 0.384

Asia WGS AF: 0.213 AC: 745 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	7.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1878528; hg19: chr4-82184234;