chr4-146578186-G-T

Variant names:

• chr4-146578186-G-T
• rs10213084

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;