chr4-155593573-T-A

Position:

• chr4-155593573-T-A

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 0.525 in 151,912 control chromosomes in the GnomAD database, including 22,032 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 0.53 (22032 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.450

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79726 AN: 151794 Hom.: 22015 Cov.: 31

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.525 AC: 79802 AN: 151912 Hom.: 22032 Cov.: 31 AF XY: 0.514 AC XY: 38135 AN XY: 74208

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.516

Alfa AF: 0.505 Hom.: 2478

Bravo AF: 0.541

Asia WGS AF: 0.349 AC: 1213 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.52
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1123037; hg19: chr4-156514725;