rs6448119

Positions:

• chr4-22089761-C-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 0.253 in 151,948 control chromosomes in the GnomAD database, including 4,884 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 0.25 (4884 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22089761C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000250039	ENST00000510705.3	n.723-11733C>T		intron_variant		5
ENSG00000250039	ENST00000665391.1	n.493-23663C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38386 AN: 151832 Hom.: 4874 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.253 AC: 38413 AN: 151948 Hom.: 4884 Cov.: 32 AF XY: 0.252 AC XY: 18691 AN XY: 74266

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.262

Alfa AF: 0.245 Hom.: 6083

Bravo AF: 0.255

Asia WGS AF: 0.357 AC: 1239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.35
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6448119; hg19: chr4-22091384;