rs1218885

Variant names:

• chr13-27523859-C-T
• rs1218885

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;