rs4835180

chr4-144599456-A-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 0.434 in 152,078 control chromosomes in the GnomAD database, including 15,496 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 0.43 (15496 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.738 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: 0.434 AC: 66000 AN: 151960 Hom.: 15485 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.434 AC: 66060 AN: 152078 Hom.: 15496 Cov.: 32 AF XY: 0.444 AC XY: 33026 AN XY: 74336

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.434

Alfa AF: 0.480 Hom.: 23197

Bravo AF: 0.421

Asia WGS AF: 0.580 AC: 2004 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.6
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4835180; hg19: chr4-145520608;