chr5-147093290-A-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000286468 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660170.1. 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
	ENSG00000286468	ENST00000660170.1		n.32A>C		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000286468	ENST00000807322.1		n.99-13A>C		intron	N/A
	ENSG00000286468	ENST00000807323.1		n.99-13A>C		intron	N/A

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

African (AFR) AF: 0.240 AC: 9975 AN: 41506

American (AMR) AF: 0.0661 AC: 1011 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0950 AC: 330 AN: 3472

East Asian (EAS) AF: 0.165 AC: 849 AN: 5158

South Asian (SAS) AF: 0.0926 AC: 447 AN: 4826

European-Finnish (FIN) AF: 0.118 AC: 1251 AN: 10602

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0747 AC: 5078 AN: 68002

Other (OTH) AF: 0.116 AC: 245 AN: 2106

Alfa AF: 0.0892 Hom.: 3389

Bravo AF: 0.128

Asia WGS AF: 0.152 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.72
DANN	Benign	0.39
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6895471; hg19: chr5-146472853;