chr4-146578186-G-T

Position:

• chr4-146578186-G-T

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 0.121 in 152,088 control chromosomes in the GnomAD database, including 1,194 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 0.12 (1194 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 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: 0.121 AC: 18346 AN: 151970 Hom.: 1192 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.0888

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0297

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.121 AC: 18360 AN: 152088 Hom.: 1194 Cov.: 32 AF XY: 0.117 AC XY: 8664 AN XY: 74340

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.0886

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.0297

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.120

Alfa AF: 0.124 Hom.: 150

Bravo AF: 0.121

Asia WGS AF: 0.0860 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10213084; hg19: chr4-147499338;