5-67246805-G-C

Position:

• chr5-67246805-G-C

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 0.548 in 152,036 control chromosomes in the GnomAD database, including 23,054 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 0.55 (23054 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354

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 (AFR) allele frequency at 95% confidence interval = 0.603 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: 0.548 AC: 83182 AN: 151916 Hom.: 23022 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.548 AC: 83263 AN: 152036 Hom.: 23054 Cov.: 32 AF XY: 0.545 AC XY: 40503 AN XY: 74306

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.546

Alfa AF: 0.413 Hom.: 1096

Bravo AF: 0.543

Asia WGS AF: 0.535 AC: 1864 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	4.5
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs984091; hg19: chr5-66542633;