rs7068170

Variant names:

• chr10-124389020-C-T
• rs7068170
• ENST00000733295.1:n.97G>A

Variant summary

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

The ENST00000733295.1(ENSG00000295867):​n.97G>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 0.274 in 152,174 control chromosomes in the GnomAD database, including 5,842 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 0.27 (5842 hom., cov: 33)
• Consequence: ENSG00000295867 ENST00000733295.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461
• Publications: 1 publications found

Genes affected

ENSG00000295867 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000733295.1. 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
	ENSG00000295867	ENST00000733295.1		n.97G>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000295867	ENST00000733296.1		n.242G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41636 AN: 152056 Hom.: 5843 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.274 AC: 41653 AN: 152174 Hom.: 5842 Cov.: 33 AF XY: 0.272 AC XY: 20203 AN XY: 74412

African (AFR) AF: 0.257 AC: 10671 AN: 41522

American (AMR) AF: 0.239 AC: 3656 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 913 AN: 3470

East Asian (EAS) AF: 0.210 AC: 1081 AN: 5156

South Asian (SAS) AF: 0.267 AC: 1290 AN: 4830

European-Finnish (FIN) AF: 0.246 AC: 2612 AN: 10606

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20468 AN: 67976

Other (OTH) AF: 0.294 AC: 622 AN: 2114

Alfa AF: 0.285 Hom.: 1267

Bravo AF: 0.275

Asia WGS AF: 0.249 AC: 867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.2
DANN	Benign	0.88
PhyloP100		-0.46

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: rs7068170;

hg19: chr10-126077589;