ENST00000702974.1:n.352G>C

Variant names:

• chr7-95396848-G-C
• rs2072200
• ENST00000702974.1:n.352G>C

Variant summary

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

The ENST00000702974.1(ENSG00000233942):​n.352G>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 0.186 in 152,196 control chromosomes in the GnomAD database, including 3,622 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 0.19 (3622 hom., cov: 32)
• Consequence: ENSG00000233942 ENST00000702974.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 12 publications found

Genes affected

ENSG00000233942 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702974.1. 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
	ENSG00000233942	ENST00000702974.1		n.352G>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000233942	ENST00000718462.1		n.409G>C		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000233942	ENST00000718463.1		n.392G>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28252 AN: 152076 Hom.: 3618 Cov.: 32

Gnomad AFR AF: 0.0664

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.186 AC: 28262 AN: 152196 Hom.: 3622 Cov.: 32 AF XY: 0.192 AC XY: 14262 AN XY: 74402

African (AFR) AF: 0.0663 AC: 2757 AN: 41554

American (AMR) AF: 0.332 AC: 5081 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 746 AN: 3470

East Asian (EAS) AF: 0.585 AC: 3005 AN: 5140

South Asian (SAS) AF: 0.257 AC: 1238 AN: 4810

European-Finnish (FIN) AF: 0.156 AC: 1653 AN: 10608

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13167 AN: 68004

Other (OTH) AF: 0.209 AC: 442 AN: 2114

Alfa AF: 0.170 Hom.: 318

Bravo AF: 0.198

Asia WGS AF: 0.385 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.54
PhyloP100		-1.0
PromoterAI		0.090	Neutral

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: rs2072200;

hg19: chr7-95026160;