5-39863861-G-T

Position:

• chr5-39863861-G-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 0.776 in 151,682 control chromosomes in the GnomAD database, including 45,968 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 0.78 (45968 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 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: 0.776 AC: 117538 AN: 151564 Hom.: 45914 Cov.: 32

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.776 AC: 117652 AN: 151682 Hom.: 45968 Cov.: 32 AF XY: 0.778 AC XY: 57653 AN XY: 74106

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.762

Gnomad4 FIN AF: 0.757

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.750

Alfa AF: 0.702 Hom.: 2375

Bravo AF: 0.782

Asia WGS AF: 0.841 AC: 2921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.27
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs506056; hg19: chr5-39863963;