5-44708276-C-G

Position:

• chr5-44708276-C-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 0.482 in 151,616 control chromosomes in the GnomAD database, including 18,404 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 0.48 (18404 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.44708276C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.481 AC: 72919 AN: 151496 Hom.: 18352 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.482 AC: 73023 AN: 151616 Hom.: 18404 Cov.: 32 AF XY: 0.486 AC XY: 35974 AN XY: 74056

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.466

Alfa AF: 0.286 Hom.: 651

Bravo AF: 0.496

Asia WGS AF: 0.572 AC: 1981 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6861560; hg19: chr5-44708378;