4-166283823-G-C

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 0.843 in 152,116 control chromosomes in the GnomAD database, including 55,671 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 0.84 (55671 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370

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 (NFE) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128106 AN: 151998 Hom.: 55655 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.951

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.843 AC: 128179 AN: 152116 Hom.: 55671 Cov.: 32 AF XY: 0.836 AC XY: 62144 AN XY: 74352

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.954

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.812

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.951

Gnomad4 OTH AF: 0.866

Alfa AF: 0.893 Hom.: 3084

Bravo AF: 0.825

Asia WGS AF: 0.600 AC: 2089 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	1.0
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: rs433130; hg19: chr4-167204975;