chr4-81228677-C-T

Variant names:

• chr4-81228677-C-T
• rs710841

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 0.365 in 151,916 control chromosomes in the GnomAD database, including 12,658 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 0.36 (12658 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358

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 = 0.645 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: 0.364 AC: 55310 AN: 151798 Hom.: 12629 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.365 AC: 55395 AN: 151916 Hom.: 12658 Cov.: 32 AF XY: 0.357 AC XY: 26511 AN XY: 74230

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.323

Alfa AF: 0.269 Hom.: 10705

Bravo AF: 0.383

Asia WGS AF: 0.219 AC: 764 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	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs710841; hg19: chr4-82149831;