rs7072122

Variant names:

• chr10-44539224-C-T
• rs7072122

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 0.055 in 152,158 control chromosomes in the GnomAD database, including 250 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 0.055 (250 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.117 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: 0.0550 AC: 8363 AN: 152040 Hom.: 254 Cov.: 33

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0252

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0332

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0541

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0550 AC: 8362 AN: 152158 Hom.: 250 Cov.: 33 AF XY: 0.0543 AC XY: 4042 AN XY: 74394

African (AFR) AF: 0.0531 AC: 2206 AN: 41516

American (AMR) AF: 0.0251 AC: 384 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 355 AN: 3472

East Asian (EAS) AF: 0.125 AC: 645 AN: 5174

South Asian (SAS) AF: 0.118 AC: 570 AN: 4826

European-Finnish (FIN) AF: 0.0332 AC: 351 AN: 10584

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0541 AC: 3677 AN: 67996

Other (OTH) AF: 0.0440 AC: 93 AN: 2112

Alfa AF: 0.0551 Hom.: 770

Bravo AF: 0.0528

Asia WGS AF: 0.0950 AC: 329 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.1
DANN	Benign	0.33
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs7072122; hg19: chr10-45034672;