4-175131343-T-C

Variant names:

• chr4-175131343-T-C
• rs330483
• ENST00000658752.1:n.90-92620A>G

Variant summary

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

The ENST00000658752.1(ENSG00000248551):​n.90-92620A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,126 control chromosomes in the GnomAD database, including 53,602 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 0.83 (53602 hom., cov: 32)
• Consequence: ENSG00000248551 ENST00000658752.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 3 publications found

Genes affected

ENSG00000248551 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248551	ENST00000658752.1	n.90-92620A>G		intron_variant	Intron 1 of 1
ENSG00000248551	ENST00000798560.1	n.349-92620A>G		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126706 AN: 152008 Hom.: 53569 Cov.: 32

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.882

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.853

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

GnomAD4 genome AF: 0.833 AC: 126794 AN: 152126 Hom.: 53602 Cov.: 32 AF XY: 0.826 AC XY: 61429 AN XY: 74358

African (AFR) AF: 0.755 AC: 31349 AN: 41504

American (AMR) AF: 0.858 AC: 13117 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3082 AN: 3472

East Asian (EAS) AF: 0.431 AC: 2222 AN: 5150

South Asian (SAS) AF: 0.665 AC: 3202 AN: 4818

European-Finnish (FIN) AF: 0.898 AC: 9504 AN: 10580

Middle Eastern (MID) AF: 0.873 AC: 255 AN: 292

European-Non Finnish (NFE) AF: 0.904 AC: 61470 AN: 68004

Other (OTH) AF: 0.851 AC: 1797 AN: 2112

Alfa AF: 0.846 Hom.: 3549

Bravo AF: 0.828

Asia WGS AF: 0.586 AC: 2035 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.25
DANN	Benign	0.53
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs330483; hg19: chr4-176052494;