chr4-155590307-G-T

Position:

• chr4-155590307-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 0.506 in 151,740 control chromosomes in the GnomAD database, including 19,782 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 0.51 (19782 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 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: 0.506 AC: 76767 AN: 151622 Hom.: 19778 Cov.: 33

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.506 AC: 76816 AN: 151740 Hom.: 19782 Cov.: 33 AF XY: 0.516 AC XY: 38277 AN XY: 74120

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.504

Alfa AF: 0.517 Hom.: 14519

Bravo AF: 0.494

Asia WGS AF: 0.633 AC: 2191 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.7
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1842896; hg19: chr4-156511459;