7-131769205-C-T

Variant names:

• chr7-131769205-C-T
• rs12534413

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 0.143 in 152,216 control chromosomes in the GnomAD database, including 1,629 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 0.14 (1629 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21747 AN: 152098 Hom.: 1630 Cov.: 33

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0890

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.143 AC: 21761 AN: 152216 Hom.: 1629 Cov.: 33 AF XY: 0.144 AC XY: 10684 AN XY: 74424

African (AFR) AF: 0.156 AC: 6478 AN: 41532

American (AMR) AF: 0.103 AC: 1569 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0890 AC: 309 AN: 3470

East Asian (EAS) AF: 0.101 AC: 522 AN: 5186

South Asian (SAS) AF: 0.108 AC: 522 AN: 4824

European-Finnish (FIN) AF: 0.193 AC: 2040 AN: 10582

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9960 AN: 68002

Other (OTH) AF: 0.124 AC: 262 AN: 2112

Alfa AF: 0.139 Hom.: 771

Bravo AF: 0.135

Asia WGS AF: 0.137 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.0
DANN	Benign	0.51
PhyloP100		-0.087

Splicing

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

Other links and lift over

dbSNP: rs12534413; hg19: chr7-131453964;