chr4-110306660-G-A

Variant names:

• chr4-110306660-G-A
• rs13148252

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 0.224 in 152,140 control chromosomes in the GnomAD database, including 4,716 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 0.22 (4716 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.373 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: 0.225 AC: 34134 AN: 152022 Hom.: 4712 Cov.: 33

Gnomad AFR AF: 0.0821

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.224 AC: 34142 AN: 152140 Hom.: 4716 Cov.: 33 AF XY: 0.225 AC XY: 16738 AN XY: 74382

Gnomad4 AFR AF: 0.0820

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.236

Alfa AF: 0.0921 Hom.: 154

Bravo AF: 0.235

Asia WGS AF: 0.215 AC: 745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13148252; hg19: chr4-111227816;