4-41297475-A-G

Position:

• chr4-41297475-A-G

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 0.0986 in 152,216 control chromosomes in the GnomAD database, including 876 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 0.099 (876 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.949

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 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: 0.0985 AC: 14985 AN: 152098 Hom.: 877 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0600

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0751

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0729

Gnomad OTH AF: 0.0824

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

GnomAD4 genome AF: 0.0986 AC: 15004 AN: 152216 Hom.: 876 Cov.: 32 AF XY: 0.0998 AC XY: 7427 AN XY: 74428

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.0599

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.0758

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.0729

Gnomad4 OTH AF: 0.0820

Alfa AF: 0.0794 Hom.: 685

Bravo AF: 0.0939

Asia WGS AF: 0.0390 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
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: rs6828613; hg19: chr4-41299492;