rs1406891

Positions:

• chr6-160766048-T-C

Variant summary

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

The ENST00000659713.1(ENSG00000287558):​n.77+1366A>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 0.609 in 152,064 control chromosomes in the GnomAD database, including 28,801 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 0.61 (28801 hom., cov: 33)
• Consequence: ENST00000659713.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000659713.1	n.77+1366A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92441 AN: 151946 Hom.: 28752 Cov.: 33

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.609 AC: 92546 AN: 152064 Hom.: 28801 Cov.: 33 AF XY: 0.615 AC XY: 45708 AN XY: 74336

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.638

Alfa AF: 0.580 Hom.: 11468

Bravo AF: 0.623

Asia WGS AF: 0.838 AC: 2908 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	1.4
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1406891; hg19: chr6-161187080;