6-16109955-C-T

Variant names:

• chr6-16109955-C-T
• rs6913929
• ENST00000806821.1:n.590-11459C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000806821.1(ENSG00000289953):​n.590-11459C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,046 control chromosomes in the GnomAD database, including 33,331 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 0.64 (33331 hom., cov: 32)
• Consequence: ENSG00000289953 ENST00000806821.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.67
• Publications: 0 publications found

Genes affected

ENSG00000289953 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806821.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289953	ENST00000806821.1		n.590-11459C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96733 AN: 151928 Hom.: 33270 Cov.: 32

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.637 AC: 96849 AN: 152046 Hom.: 33331 Cov.: 32 AF XY: 0.635 AC XY: 47212 AN XY: 74298

African (AFR) AF: 0.890 AC: 36929 AN: 41486

American (AMR) AF: 0.631 AC: 9633 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2026 AN: 3472

East Asian (EAS) AF: 0.903 AC: 4675 AN: 5180

South Asian (SAS) AF: 0.655 AC: 3157 AN: 4822

European-Finnish (FIN) AF: 0.459 AC: 4851 AN: 10560

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33763 AN: 67946

Other (OTH) AF: 0.593 AC: 1247 AN: 2104

Alfa AF: 0.552 Hom.: 5195

Bravo AF: 0.662

Asia WGS AF: 0.816 AC: 2839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.14
DANN	Benign	0.40
PhyloP100		-4.7

Splicing

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

Other links and lift over

dbSNP: rs6913929; hg19: chr6-16110186;