rs1218897

Variant names:

• chr13-27505637-T-C
• rs1218897

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 0.397 in 152,096 control chromosomes in the GnomAD database, including 12,878 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 0.40 (12878 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.766
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 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: 0.397 AC: 60345 AN: 151978 Hom.: 12879 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.397 AC: 60360 AN: 152096 Hom.: 12878 Cov.: 32 AF XY: 0.402 AC XY: 29849 AN XY: 74320

African (AFR) AF: 0.240 AC: 9954 AN: 41480

American (AMR) AF: 0.460 AC: 7029 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1747 AN: 3472

East Asian (EAS) AF: 0.523 AC: 2703 AN: 5166

South Asian (SAS) AF: 0.508 AC: 2445 AN: 4816

European-Finnish (FIN) AF: 0.456 AC: 4821 AN: 10568

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30237 AN: 67998

Other (OTH) AF: 0.429 AC: 907 AN: 2112

Alfa AF: 0.434 Hom.: 6559

Bravo AF: 0.390

Asia WGS AF: 0.458 AC: 1594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	14
DANN	Benign	0.64
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs1218897; hg19: chr13-28079774;