rs7234352

Variant names:

• chr18-63072000-A-G
• rs7234352
• ENST00000763628.1:n.235-18335A>G

Variant summary

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

The ENST00000763628.1(ENSG00000299452):​n.235-18335A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,110 control chromosomes in the GnomAD database, including 10,596 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 0.34 (10596 hom., cov: 32)
• Consequence: ENSG00000299452 ENST00000763628.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 2 publications found

Genes affected

ENSG00000299452 (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 (AFR) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000763628.1. 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
	ENSG00000299452	ENST00000763628.1		n.235-18335A>G		intron	N/A
	ENSG00000299452	ENST00000763629.1		n.235-24013A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52318 AN: 151990 Hom.: 10563 Cov.: 32

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.344 AC: 52400 AN: 152110 Hom.: 10596 Cov.: 32 AF XY: 0.342 AC XY: 25408 AN XY: 74358

African (AFR) AF: 0.538 AC: 22314 AN: 41468

American (AMR) AF: 0.395 AC: 6040 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 787 AN: 3470

East Asian (EAS) AF: 0.482 AC: 2500 AN: 5186

South Asian (SAS) AF: 0.289 AC: 1394 AN: 4822

European-Finnish (FIN) AF: 0.214 AC: 2265 AN: 10580

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.236 AC: 16066 AN: 67986

Other (OTH) AF: 0.308 AC: 650 AN: 2110

Alfa AF: 0.285 Hom.: 13146

Bravo AF: 0.372

Asia WGS AF: 0.393 AC: 1365 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	0.059
DANN	Benign	0.27
PhyloP100		-2.2

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: rs7234352;

hg19: chr18-60739233;