rs10872573

Variant names:

• chr6-100362746-T-C
• rs10872573

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.732 AC: 30301 AN: 41378

American (AMR) AF: 0.526 AC: 8016 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2280 AN: 3470

East Asian (EAS) AF: 0.361 AC: 1857 AN: 5142

South Asian (SAS) AF: 0.655 AC: 3153 AN: 4812

European-Finnish (FIN) AF: 0.614 AC: 6470 AN: 10542

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48507 AN: 67928

Other (OTH) AF: 0.706 AC: 1491 AN: 2112

Alfa AF: 0.690 Hom.: 18456

Bravo AF: 0.672

Asia WGS AF: 0.566 AC: 1971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.6
DANN	Benign	0.70
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10872573; hg19: chr6-100810622;