rs1074442

Positions:

• chr4-183573618-T-A
• chr4-183573618-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;