rs10872573

Variant names:

• chr6-100362746-T-C
• rs10872573

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;