6-164070022-T-C

Variant names:

• chr6-164070022-T-C
• rs206694
• ENST00000850166.1:n.997T>C

Variant summary

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

The ENST00000850166.1(ENSG00000288696):​n.997T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 152,230 control chromosomes in the GnomAD database, including 50,934 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 0.82 (50934 hom., cov: 33)
• Consequence: ENSG00000288696 ENST00000850166.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 5 publications found

Genes affected

ENSG00000288696 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 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
ENSG00000288696	ENST00000850166.1	n.997T>C		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000288696	ENST00000850151.1	n.311+11056T>C		intron_variant	Intron 3 of 4
ENSG00000288696	ENST00000850152.1	n.371+11056T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.815 AC: 123959 AN: 152114 Hom.: 50881 Cov.: 33

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.815 AC: 124070 AN: 152230 Hom.: 50934 Cov.: 33 AF XY: 0.819 AC XY: 60987 AN XY: 74426

African (AFR) AF: 0.914 AC: 37963 AN: 41546

American (AMR) AF: 0.824 AC: 12606 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2771 AN: 3472

East Asian (EAS) AF: 0.793 AC: 4109 AN: 5180

South Asian (SAS) AF: 0.816 AC: 3935 AN: 4820

European-Finnish (FIN) AF: 0.821 AC: 8691 AN: 10584

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51262 AN: 68014

Other (OTH) AF: 0.817 AC: 1724 AN: 2110

Alfa AF: 0.814 Hom.: 9727

Bravo AF: 0.823

Asia WGS AF: 0.816 AC: 2837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	14
DANN	Benign	0.86
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs206694; hg19: chr6-164491054; COSMIC: COSV60300420;