4-171483944-T-G

Variant names:

• chr4-171483944-T-G
• rs4144862

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 0.413 in 151,802 control chromosomes in the GnomAD database, including 19,251 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 0.41 (19251 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 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: 0.412 AC: 62566 AN: 151684 Hom.: 19192 Cov.: 32

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.413 AC: 62682 AN: 151802 Hom.: 19251 Cov.: 32 AF XY: 0.412 AC XY: 30539 AN XY: 74208

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.368

Alfa AF: 0.221 Hom.: 6273

Bravo AF: 0.452

Asia WGS AF: 0.482 AC: 1676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4144862; hg19: chr4-172405095;