chr6-168717241-G-T

Variant names:

• chr6-168717241-G-T
• rs196458
• ENST00000747060.1:n.1333C>A

Variant summary

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

The ENST00000747060.1(ENSG00000297313):​n.1333C>A 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 0.932 in 151,856 control chromosomes in the GnomAD database, including 65,989 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 (65989 hom., cov: 29)
• Consequence: ENSG00000297313 ENST00000747060.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150
• Publications: 2 publications found

Genes affected

ENSG00000297313 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=1.857).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378143	XR_001744472.2	n.6478G>T		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105378143	XR_943296.3	n.6748G>T		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297313	ENST00000747060.1	n.1333C>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000289090	ENST00000436492.1	n.80+556G>T		intron_variant	Intron 1 of 2	3
ENSG00000289090	ENST00000746859.1	n.309-3721G>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.932 AC: 141411 AN: 151738 Hom.: 65947 Cov.: 29

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.940

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

GnomAD4 genome AF: 0.932 AC: 141513 AN: 151856 Hom.: 65989 Cov.: 29 AF XY: 0.931 AC XY: 69075 AN XY: 74172

African (AFR) AF: 0.966 AC: 40016 AN: 41434

American (AMR) AF: 0.916 AC: 13990 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3175 AN: 3472

East Asian (EAS) AF: 0.961 AC: 4890 AN: 5086

South Asian (SAS) AF: 0.951 AC: 4553 AN: 4790

European-Finnish (FIN) AF: 0.920 AC: 9713 AN: 10554

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.913 AC: 62054 AN: 67934

Other (OTH) AF: 0.939 AC: 1981 AN: 2110

Alfa AF: 0.925 Hom.: 8405

Bravo AF: 0.934

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	1.9
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs196458; hg19: -;