rs7987146

Variant names:

• chr13-103429614-T-C
• rs7987146

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 0.215 in 151,994 control chromosomes in the GnomAD database, including 3,787 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 0.21 (3787 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 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: 0.214 AC: 32570 AN: 151876 Hom.: 3774 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.215 AC: 32611 AN: 151994 Hom.: 3787 Cov.: 32 AF XY: 0.212 AC XY: 15743 AN XY: 74326

African (AFR) AF: 0.324 AC: 13400 AN: 41408

American (AMR) AF: 0.134 AC: 2041 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3472

East Asian (EAS) AF: 0.151 AC: 782 AN: 5162

South Asian (SAS) AF: 0.144 AC: 692 AN: 4818

European-Finnish (FIN) AF: 0.174 AC: 1838 AN: 10580

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12883 AN: 67962

Other (OTH) AF: 0.205 AC: 432 AN: 2110

Alfa AF: 0.195 Hom.: 12723

Bravo AF: 0.215

Asia WGS AF: 0.161 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.6
DANN	Benign	0.88
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs7987146; hg19: chr13-104081964;