chr4-183360114-C-T

Position:

• chr4-183360114-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 0.582 in 151,462 control chromosomes in the GnomAD database, including 26,039 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 0.58 (26039 hom., cov: 28)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

Genes affected

(HGNC:):

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 = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.183360114C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88061 AN: 151344 Hom.: 26027 Cov.: 28

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.667

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.582 AC: 88108 AN: 151462 Hom.: 26039 Cov.: 28 AF XY: 0.586 AC XY: 43380 AN XY: 73984

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.588

Alfa AF: 0.558 Hom.: 5108

Bravo AF: 0.591

Asia WGS AF: 0.662 AC: 2300 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1113122; hg19: chr4-184281267;