5-169472983-T-C

Position:

• chr5-169472983-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 0.651 in 152,046 control chromosomes in the GnomAD database, including 32,730 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 0.65 (32730 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.169472983T>C		intergenic_region
LOC105377714	XR_941200.3	n.461-13047A>G		intron_variant
LOC105377715	XR_941204.3	n.241-1442T>C		intron_variant
LOC105377715	XR_941205.3	n.230+3743T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98954 AN: 151928 Hom.: 32698 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.651 AC: 99039 AN: 152046 Hom.: 32730 Cov.: 32 AF XY: 0.655 AC XY: 48662 AN XY: 74328

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.971

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.664

Alfa AF: 0.653 Hom.: 59831

Bravo AF: 0.664

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13156607; hg19: chr5-168899987;