rs6869841

Positions:

• chr5-173512423-C-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 0.255 in 152,142 control chromosomes in the GnomAD database, including 5,345 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 0.25 (5345 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

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 (AFR) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.173512423C>T		intergenic_region
LOC105377732	XR_001743001.1	n.3056+4833C>T		intron_variant
LOC105377732	XR_007059057.1	n.4116+4833C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38714 AN: 152024 Hom.: 5338 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.255 AC: 38751 AN: 152142 Hom.: 5345 Cov.: 32 AF XY: 0.252 AC XY: 18720 AN XY: 74386

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.252

Alfa AF: 0.224 Hom.: 922

Bravo AF: 0.258

Asia WGS AF: 0.223 AC: 778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6869841; hg19: chr5-172939426;