rs1218885

chr13-27523859-C-T

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 0.389 in 152,132 control chromosomes in the GnomAD database, including 12,676 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 0.39 (12676 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59207 AN: 152014 Hom.: 12677 Cov.: 33

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.389 AC: 59211 AN: 152132 Hom.: 12676 Cov.: 33 AF XY: 0.395 AC XY: 29387 AN XY: 74356

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.424

Alfa AF: 0.442 Hom.: 31079

Bravo AF: 0.382

Asia WGS AF: 0.473 AC: 1647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.5
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1218885; hg19: chr13-28097996;