13-67997905-C-G

Position:

• chr13-67997905-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0411 in 151,956 control chromosomes in the GnomAD database, including 170 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 0.041 (170 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0412 AC: 6249 AN: 151838 Hom.: 171 Cov.: 32

Gnomad AFR AF: 0.0139

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.0659

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.00912

Gnomad FIN AF: 0.0351

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0566

Gnomad OTH AF: 0.0654

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

GnomAD4 genome AF: 0.0411 AC: 6247 AN: 151956 Hom.: 170 Cov.: 32 AF XY: 0.0401 AC XY: 2981 AN XY: 74266

Gnomad4 AFR AF: 0.0139

Gnomad4 AMR AF: 0.0657

Gnomad4 ASJ AF: 0.0562

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.00912

Gnomad4 FIN AF: 0.0351

Gnomad4 NFE AF: 0.0566

Gnomad4 OTH AF: 0.0648

Alfa AF: 0.0439 Hom.: 28

Bravo AF: 0.0429

Asia WGS AF: 0.00665 AC: 23 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.56
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7318913; hg19: chr13-68572037;