5-9978972-T-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 0.679 in 152,146 control chromosomes in the GnomAD database, including 35,308 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 0.68 (35308 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 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: 0.679 AC: 103215 AN: 152028 Hom.: 35266 Cov.: 33

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.679 AC: 103314 AN: 152146 Hom.: 35308 Cov.: 33 AF XY: 0.678 AC XY: 50465 AN XY: 74382

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.683

Alfa AF: 0.708 Hom.: 38718

Bravo AF: 0.685

Asia WGS AF: 0.700 AC: 2436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.5
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs553169; hg19: chr5-9979084;