13-26727717-G-C

Variant names:

• chr13-26727717-G-C
• rs2441075

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;