ENST00000670475.1:n.928C>A

Variant names:

• chr13-63437530-C-A
• rs1905471
• ENST00000670475.1:n.928C>A

Variant summary

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

The ENST00000670475.1(ENSG00000287996):​n.928C>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 0.177 in 151,888 control chromosomes in the GnomAD database, including 2,865 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 (2865 hom., cov: 31)
• Consequence: ENSG00000287996 ENST00000670475.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188
• Publications: 1 publications found

Genes affected

ENSG00000287996 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670475.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287996	ENST00000670475.1		n.928C>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000287996	ENST00000652818.1		n.415+40008C>A		intron	N/A
	ENSG00000287996	ENST00000656278.1		n.296-3879C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26762 AN: 151770 Hom.: 2850 Cov.: 31

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.177 AC: 26816 AN: 151888 Hom.: 2865 Cov.: 31 AF XY: 0.182 AC XY: 13530 AN XY: 74194

African (AFR) AF: 0.190 AC: 7877 AN: 41442

American (AMR) AF: 0.216 AC: 3295 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3472

East Asian (EAS) AF: 0.567 AC: 2895 AN: 5106

South Asian (SAS) AF: 0.226 AC: 1084 AN: 4806

European-Finnish (FIN) AF: 0.160 AC: 1695 AN: 10564

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8959 AN: 67964

Other (OTH) AF: 0.184 AC: 388 AN: 2104

Alfa AF: 0.158 Hom.: 246

Bravo AF: 0.184

Asia WGS AF: 0.355 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.7
DANN	Benign	0.76
PhyloP100		0.19

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1905471;

hg19: chr13-64011663;