ENST00000660170.1:n.32A>C

Variant names:

• chr5-147093290-A-C
• rs6895471
• ENST00000660170.1:n.32A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000660170.1(ENSG00000286468):​n.32A>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 0.127 in 152,164 control chromosomes in the GnomAD database, including 1,597 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 0.13 (1597 hom., cov: 33)
• Consequence: ENSG00000286468 ENST00000660170.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

ENSG00000286468 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 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
ENSG00000286468	ENST00000660170.1	n.32A>C		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19267 AN: 152044 Hom.: 1588 Cov.: 33

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0662

Gnomad ASJ AF: 0.0950

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.0928

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0747

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.127 AC: 19311 AN: 152164 Hom.: 1597 Cov.: 33 AF XY: 0.127 AC XY: 9446 AN XY: 74370

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.0661

Gnomad4 ASJ AF: 0.0950

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.0926

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.0747

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0804 Hom.: 1268

Bravo AF: 0.128

Asia WGS AF: 0.152 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.72
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6895471; hg19: chr5-146472853;