rs407218

Variant names:

• chr13-85872489-G-A
• rs407218

Your query was ambiguous. Multiple possible variants found:

• chr13-85872489-G-A
• chr13-85872489-G-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 0.493 in 151,682 control chromosomes in the GnomAD database, including 20,596 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 0.49 (20596 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 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: 0.493 AC: 74752 AN: 151564 Hom.: 20591 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.493 AC: 74785 AN: 151682 Hom.: 20596 Cov.: 32 AF XY: 0.498 AC XY: 36933 AN XY: 74140

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.502

Alfa AF: 0.545 Hom.: 2928

Bravo AF: 0.463

Asia WGS AF: 0.590 AC: 2051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs407218; hg19: chr13-86446624;