rs13205238

chr6-468597-A-Gchr6-468597-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, non coding transcript 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: ENST00000661640.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.19

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661640.1	n.336-6611A>G		intron_variant, non_coding_transcript_variant

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;