13-26727717-G-C

Position:

• chr13-26727717-G-C

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 0.471 in 150,996 control chromosomes in the GnomAD database, including 17,082 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 0.47 (17082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 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: 0.472 AC: 71143 AN: 150880 Hom.: 17065 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.471 AC: 71194 AN: 150996 Hom.: 17082 Cov.: 32 AF XY: 0.469 AC XY: 34597 AN XY: 73696

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.512

Alfa AF: 0.318 Hom.: 762

Bravo AF: 0.469

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.68
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2441075; hg19: chr13-27301854;