7-127443075-T-C

Variant names:

• chr7-127443075-T-C
• rs12673058

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 0.327 in 151,708 control chromosomes in the GnomAD database, including 10,254 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 0.33 (10254 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.709 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: 0.328 AC: 49668 AN: 151590 Hom.: 10242 Cov.: 30

Gnomad AFR AF: 0.0908

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.327 AC: 49680 AN: 151708 Hom.: 10254 Cov.: 30 AF XY: 0.336 AC XY: 24904 AN XY: 74098

African (AFR) AF: 0.0906 AC: 3754 AN: 41432

American (AMR) AF: 0.380 AC: 5773 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 927 AN: 3468

East Asian (EAS) AF: 0.728 AC: 3754 AN: 5154

South Asian (SAS) AF: 0.407 AC: 1949 AN: 4794

European-Finnish (FIN) AF: 0.468 AC: 4889 AN: 10454

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27524 AN: 67890

Other (OTH) AF: 0.327 AC: 689 AN: 2106

Alfa AF: 0.364 Hom.: 1439

Bravo AF: 0.312

Asia WGS AF: 0.520 AC: 1802 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	3.9
DANN	Benign	0.76
PhyloP100		-0.059

Splicing

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

Other links and lift over

dbSNP: rs12673058; hg19: chr7-127083129;