rs4446414

Positions:

• chr5-62949231-G-A

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 0.0191 in 152,218 control chromosomes in the GnomAD database, including 64 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 0.019 (64 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.62949231G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0191 AC: 2898 AN: 152100 Hom.: 63 Cov.: 32

Gnomad AFR AF: 0.0297

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0149

Gnomad ASJ AF: 0.00865

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0670

Gnomad FIN AF: 0.00151

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00737

Gnomad OTH AF: 0.0182

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

GnomAD4 genome AF: 0.0191 AC: 2911 AN: 152218 Hom.: 64 Cov.: 32 AF XY: 0.0195 AC XY: 1453 AN XY: 74420

Gnomad4 AFR AF: 0.0298

Gnomad4 AMR AF: 0.0149

Gnomad4 ASJ AF: 0.00865

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0675

Gnomad4 FIN AF: 0.00151

Gnomad4 NFE AF: 0.00737

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.0116 Hom.: 2

Bravo AF: 0.0196

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4446414; hg19: chr5-62245058;