chr4-189227641-C-A

Variant names:

• chr4-189227641-C-A
• rs10446846

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 0.782 in 152,112 control chromosomes in the GnomAD database, including 47,433 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 0.78 (47433 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.829

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.856 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: 0.782 AC: 118801 AN: 151994 Hom.: 47400 Cov.: 32

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.782 AC: 118887 AN: 152112 Hom.: 47433 Cov.: 32 AF XY: 0.784 AC XY: 58291 AN XY: 74372

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.876

Gnomad4 SAS AF: 0.791

Gnomad4 FIN AF: 0.915

Gnomad4 NFE AF: 0.862

Gnomad4 OTH AF: 0.784

Alfa AF: 0.838 Hom.: 64120

Bravo AF: 0.764

Asia WGS AF: 0.847 AC: 2946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.34
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10446846; hg19: chr4-190148795;