10-30488351-G-T

Variant names:

• chr10-30488351-G-T
• rs303451
• ENST00000824991.1:n.705C>A

Variant summary

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

The ENST00000824991.1(ENSG00000307302):​n.705C>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 0.894 in 152,216 control chromosomes in the GnomAD database, including 60,958 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 0.89 (60958 hom., cov: 31)
• Consequence: ENSG00000307302 ENST00000824991.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251
• Publications: 6 publications found

Genes affected

ENSG00000307302 (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 = 0.94 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824991.1. 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
	ENSG00000307302	ENST00000824991.1		n.705C>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.894 AC: 135983 AN: 152098 Hom.: 60895 Cov.: 31

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.850

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.894 AC: 136104 AN: 152216 Hom.: 60958 Cov.: 31 AF XY: 0.894 AC XY: 66488 AN XY: 74406

African (AFR) AF: 0.930 AC: 38611 AN: 41522

American (AMR) AF: 0.903 AC: 13815 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3052 AN: 3470

East Asian (EAS) AF: 0.963 AC: 4984 AN: 5178

South Asian (SAS) AF: 0.779 AC: 3761 AN: 4828

European-Finnish (FIN) AF: 0.879 AC: 9308 AN: 10594

Middle Eastern (MID) AF: 0.853 AC: 249 AN: 292

European-Non Finnish (NFE) AF: 0.877 AC: 59677 AN: 68012

Other (OTH) AF: 0.882 AC: 1860 AN: 2110

Alfa AF: 0.878 Hom.: 43260

Bravo AF: 0.897

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.35
PhyloP100		0.25

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: rs303451;

hg19: chr10-30777280;