chr5-133729269-C-T

Position:

• chr5-133729269-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011543283.2(FSTL4):​c.-11+112683G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,788 control chromosomes in the GnomAD database, including 2,650 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 0.15 (2650 hom., cov: 31)
• Consequence: FSTL4 XM_011543283.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523

Genes affected

FSTL4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSTL4	XM_011543283.2	c.-11+112683G>A		intron_variant			XP_011541585.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23233 AN: 151670 Hom.: 2642 Cov.: 31

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0925

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.00790

Gnomad SAS AF: 0.0571

Gnomad FIN AF: 0.0677

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.153 AC: 23251 AN: 151788 Hom.: 2650 Cov.: 31 AF XY: 0.148 AC XY: 11014 AN XY: 74172

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.0924

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.00792

Gnomad4 SAS AF: 0.0569

Gnomad4 FIN AF: 0.0677

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.120

Alfa AF: 0.106 Hom.: 1301

Bravo AF: 0.162

Asia WGS AF: 0.0580 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.4
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6870951; hg19: chr5-133064960;