5-44708276-C-G

Variant names:

• chr5-44708276-C-G
• rs6861560

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;