5-107782439-G-T

Variant names:

• chr5-107782439-G-T
• rs770182

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 0.666 in 151,954 control chromosomes in the GnomAD database, including 33,797 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 0.67 (33797 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 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: 0.666 AC: 101088 AN: 151834 Hom.: 33751 Cov.: 31

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.666 AC: 101186 AN: 151954 Hom.: 33797 Cov.: 31 AF XY: 0.662 AC XY: 49181 AN XY: 74268

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.679

Alfa AF: 0.692 Hom.: 73474

Bravo AF: 0.676

Asia WGS AF: 0.742 AC: 2582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.82
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs770182; hg19: chr5-107118140; COSMIC: COSV69025974;