10-72045532-C-G

Variant names:

• chr10-72045532-C-G
• rs1612028

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 0.391 in 152,012 control chromosomes in the GnomAD database, including 12,557 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 0.39 (12557 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.327
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 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: 0.391 AC: 59371 AN: 151894 Hom.: 12558 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.391 AC: 59369 AN: 152012 Hom.: 12557 Cov.: 32 AF XY: 0.383 AC XY: 28463 AN XY: 74274

African (AFR) AF: 0.250 AC: 10370 AN: 41450

American (AMR) AF: 0.393 AC: 6008 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1770 AN: 3470

East Asian (EAS) AF: 0.113 AC: 583 AN: 5182

South Asian (SAS) AF: 0.296 AC: 1422 AN: 4812

European-Finnish (FIN) AF: 0.432 AC: 4552 AN: 10538

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33164 AN: 67974

Other (OTH) AF: 0.431 AC: 907 AN: 2106

Alfa AF: 0.289 Hom.: 752

Bravo AF: 0.382

Asia WGS AF: 0.209 AC: 730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.3
DANN	Benign	0.59
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs1612028; hg19: chr10-73805290;