rs10872573

Positions:

• chr6-100362746-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 0.678 in 151,820 control chromosomes in the GnomAD database, including 35,614 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 (35614 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.100362746T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102922 AN: 151700 Hom.: 35585 Cov.: 30

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.678 AC: 102995 AN: 151820 Hom.: 35614 Cov.: 30 AF XY: 0.668 AC XY: 49538 AN XY: 74170

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.706

Alfa AF: 0.686 Hom.: 16247

Bravo AF: 0.672

Asia WGS AF: 0.566 AC: 1971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.6
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10872573; hg19: chr6-100810622;