6-16018884-T-C

Variant names:

• chr6-16018884-T-C
• rs6921953
• ENST00000806821.1:n.449-15047T>C

Variant summary

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

The ENST00000806821.1(ENSG00000289953):​n.449-15047T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.93 in 152,302 control chromosomes in the GnomAD database, including 66,021 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 0.93 (66021 hom., cov: 35)
• Consequence: ENSG00000289953 ENST00000806821.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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.449-15047T>C		intron	N/A
	ENSG00000289953	ENST00000806822.1		n.463-15047T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.930 AC: 141604 AN: 152184 Hom.: 65975 Cov.: 35

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.959

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.930

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.948

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.930 AC: 141708 AN: 152302 Hom.: 66021 Cov.: 35 AF XY: 0.928 AC XY: 69123 AN XY: 74460

African (AFR) AF: 0.883 AC: 36707 AN: 41566

American (AMR) AF: 0.959 AC: 14688 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.965 AC: 3351 AN: 3472

East Asian (EAS) AF: 0.995 AC: 5135 AN: 5160

South Asian (SAS) AF: 0.931 AC: 4491 AN: 4824

European-Finnish (FIN) AF: 0.915 AC: 9709 AN: 10616

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.948 AC: 64506 AN: 68036

Other (OTH) AF: 0.926 AC: 1955 AN: 2112

Alfa AF: 0.943 Hom.: 115415

Bravo AF: 0.935

Asia WGS AF: 0.952 AC: 3313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.32
DANN	Benign	0.64
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs6921953; hg19: chr6-16019115;