rs1218885

Variant names:

• chr13-27523859-C-T
• rs1218885

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.206 AC: 8569 AN: 41520

American (AMR) AF: 0.465 AC: 7119 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1711 AN: 3470

East Asian (EAS) AF: 0.568 AC: 2927 AN: 5154

South Asian (SAS) AF: 0.531 AC: 2556 AN: 4816

European-Finnish (FIN) AF: 0.442 AC: 4687 AN: 10594

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30249 AN: 67964

Other (OTH) AF: 0.424 AC: 895 AN: 2110

Alfa AF: 0.430 Hom.: 61262

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
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1218885; hg19: chr13-28097996;