7-13832599-T-G

Variant names:

• chr7-13832599-T-G
• rs13437998

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 0.338 in 152,094 control chromosomes in the GnomAD database, including 8,810 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 0.34 (8810 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600
• Publications: 1 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 (AMR) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51347 AN: 151976 Hom.: 8802 Cov.: 33

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.338 AC: 51370 AN: 152094 Hom.: 8810 Cov.: 33 AF XY: 0.340 AC XY: 25278 AN XY: 74342

African (AFR) AF: 0.308 AC: 12764 AN: 41498

American (AMR) AF: 0.437 AC: 6673 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3468

East Asian (EAS) AF: 0.345 AC: 1785 AN: 5180

South Asian (SAS) AF: 0.301 AC: 1451 AN: 4822

European-Finnish (FIN) AF: 0.351 AC: 3707 AN: 10558

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22932 AN: 67984

Other (OTH) AF: 0.319 AC: 674 AN: 2112

Alfa AF: 0.219 Hom.: 506

Bravo AF: 0.344

Asia WGS AF: 0.311 AC: 1079 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.8
DANN	Benign	0.65
PhyloP100		-0.060

Splicing

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

Other links and lift over

dbSNP: rs13437998; hg19: chr7-13872224;