rs13205238

Variant names:

• chr6-468597-A-G
• rs13205238
• ENST00000661640.1:n.336-6611A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-468597-A-G
• chr6-468597-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661640.1(ENSG00000286364):​n.336-6611A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 151,548 control chromosomes in the GnomAD database, including 48,011 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 0.78 (48011 hom., cov: 29)
• Consequence: ENSG00000286364 ENST00000661640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.19

Genes affected

ENSG00000286364 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.896 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
ENSG00000286364	ENST00000661640.1	n.336-6611A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118259 AN: 151430 Hom.: 47982 Cov.: 29

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.961

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.781 AC: 118347 AN: 151548 Hom.: 48011 Cov.: 29 AF XY: 0.780 AC XY: 57706 AN XY: 74016

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.872

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.739

Gnomad4 FIN AF: 0.905

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.811

Alfa AF: 0.872 Hom.: 36363

Bravo AF: 0.763

Asia WGS AF: 0.707 AC: 2460 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	0.23
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13205238; hg19: chr6-468597;