ENST00000800210.1:n.434A>G

Variant names:

• chr7-128822793-T-C
• rs58845495
• ENST00000800210.1:n.434A>G

Variant summary

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

The ENST00000800210.1(ENSG00000304163):​n.434A>G 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 0.094 in 152,126 control chromosomes in the GnomAD database, including 690 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 0.094 (690 hom., cov: 32)
• Consequence: ENSG00000304163 ENST00000800210.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 4 publications found

Genes affected

ENSG00000304163 (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 (EAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000800210.1. 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
	ENSG00000304163	ENST00000800210.1		n.434A>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000304163	ENST00000800211.1		n.258A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000304163	ENST00000800212.1		n.380A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0940 AC: 14282 AN: 152008 Hom.: 688 Cov.: 32

Gnomad AFR AF: 0.0980

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.0885

Gnomad ASJ AF: 0.0988

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.0847

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0863

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0940 AC: 14302 AN: 152126 Hom.: 690 Cov.: 32 AF XY: 0.0941 AC XY: 6996 AN XY: 74362

African (AFR) AF: 0.0981 AC: 4071 AN: 41516

American (AMR) AF: 0.0884 AC: 1352 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0988 AC: 343 AN: 3470

East Asian (EAS) AF: 0.191 AC: 980 AN: 5142

South Asian (SAS) AF: 0.0999 AC: 482 AN: 4826

European-Finnish (FIN) AF: 0.0847 AC: 897 AN: 10590

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0863 AC: 5867 AN: 67982

Other (OTH) AF: 0.107 AC: 225 AN: 2106

Alfa AF: 0.0937 Hom.: 87

Bravo AF: 0.0953

Asia WGS AF: 0.148 AC: 513 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	4.5
DANN	Benign	0.63
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs58845495; hg19: chr7-128462847;