chr4-183573618-T-A

Variant names:

• chr4-183573618-T-A
• rs1074442

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 0.185 in 151,952 control chromosomes in the GnomAD database, including 2,774 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 0.18 (2774 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.184 AC: 28000 AN: 151834 Hom.: 2767 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.0756

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.185 AC: 28039 AN: 151952 Hom.: 2774 Cov.: 32 AF XY: 0.186 AC XY: 13838 AN XY: 74280

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.0756

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.202

Alfa AF: 0.162 Hom.: 240

Bravo AF: 0.195

Asia WGS AF: 0.270 AC: 937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1074442; hg19: chr4-184494771;