4-23343831-T-G

Position:

• chr4-23343831-T-G

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 0.358 in 151,910 control chromosomes in the GnomAD database, including 11,075 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 0.36 (11075 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.23343831T>G		intergenic_region
LOC105374523	XR_001741614.1	n.227-14388A>C		intron_variant
LOC105374524	XR_007058437.1	n.2932+10305T>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54427 AN: 151792 Hom.: 11071 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.358 AC: 54441 AN: 151910 Hom.: 11075 Cov.: 33 AF XY: 0.361 AC XY: 26761 AN XY: 74220

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.375

Alfa AF: 0.423 Hom.: 22978

Bravo AF: 0.350

Asia WGS AF: 0.434 AC: 1508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	10
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1396669; hg19: chr4-23345454;