rs4444930

Positions:

• chr5-180981830-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 0.0561 in 134,520 control chromosomes in the GnomAD database, including 1,821 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 0.056 (1821 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.598

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0879 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0562 AC: 7550 AN: 134414 Hom.: 1822 Cov.: 24

Gnomad AFR AF: 0.0123

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.0475

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.000439

Gnomad SAS AF: 0.0461

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.0899

Gnomad OTH AF: 0.0588

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

GnomAD4 genome AF: 0.0561 AC: 7547 AN: 134520 Hom.: 1821 Cov.: 24 AF XY: 0.0560 AC XY: 3665 AN XY: 65434

Gnomad4 AFR AF: 0.0123

Gnomad4 AMR AF: 0.0474

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.000440

Gnomad4 SAS AF: 0.0466

Gnomad4 FIN AF: 0.0758

Gnomad4 NFE AF: 0.0899

Gnomad4 OTH AF: 0.0565

Alfa AF: 0.0530 Hom.: 179

Asia WGS AF: 0.0280 AC: 94 AN: 3320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4444930; hg19: chr5-180408830;