7-130379650-T-C

Variant names:

• chr7-130379650-T-C
• rs13226219

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 0.0961 in 152,206 control chromosomes in the GnomAD database, including 817 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 0.096 (817 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.475
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0961 AC: 14609 AN: 152088 Hom.: 816 Cov.: 32

Gnomad AFR AF: 0.0437

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.0786

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0942

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0961 AC: 14629 AN: 152206 Hom.: 817 Cov.: 32 AF XY: 0.0963 AC XY: 7166 AN XY: 74424

African (AFR) AF: 0.0442 AC: 1836 AN: 41546

American (AMR) AF: 0.0863 AC: 1320 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0786 AC: 273 AN: 3472

East Asian (EAS) AF: 0.178 AC: 917 AN: 5162

South Asian (SAS) AF: 0.183 AC: 882 AN: 4824

European-Finnish (FIN) AF: 0.0942 AC: 999 AN: 10608

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8046 AN: 67990

Other (OTH) AF: 0.104 AC: 219 AN: 2110

Alfa AF: 0.110 Hom.: 1431

Bravo AF: 0.0900

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.55
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs13226219; hg19: chr7-130019491;