ENST00000447311.1:n.365-1092C>T

Variant names:

• chr6-142529475-G-A
• rs171891
• ENST00000447311.1:n.365-1092C>T

Variant summary

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

The ENST00000447311.1(ENSG00000236366):​n.365-1092C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,024 control chromosomes in the GnomAD database, including 2,396 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 0.18 (2396 hom., cov: 31)
• Consequence: ENSG00000236366 ENST00000447311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 8 publications found

Genes affected

ENSG00000236366 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447311.1. 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
	LOC153910	NR_027311.1		n.362-1092C>T		intron	N/A
	LOC153910	NR_027312.1		n.365-1092C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000236366	ENST00000447311.1	TSL:2	n.365-1092C>T		intron	N/A
	ENSG00000236366	ENST00000635073.1	TSL:4	n.488-1092C>T		intron	N/A
	ENSG00000236366	ENST00000654741.1		n.27-1092C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.178 AC: 26980 AN: 151906 Hom.: 2392 Cov.: 31

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.178 AC: 27010 AN: 152024 Hom.: 2396 Cov.: 31 AF XY: 0.179 AC XY: 13331 AN XY: 74300

African (AFR) AF: 0.167 AC: 6941 AN: 41476

American (AMR) AF: 0.176 AC: 2682 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 646 AN: 3468

East Asian (EAS) AF: 0.106 AC: 549 AN: 5156

South Asian (SAS) AF: 0.242 AC: 1166 AN: 4816

European-Finnish (FIN) AF: 0.199 AC: 2104 AN: 10568

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12349 AN: 67950

Other (OTH) AF: 0.184 AC: 389 AN: 2116

Alfa AF: 0.171 Hom.: 1790

Bravo AF: 0.171

Asia WGS AF: 0.213 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.8
DANN	Benign	0.57
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs171891; hg19: chr6-142850612;