chr4-175159931-T-C

Variant names:

• chr4-175159931-T-C
• rs330504
• ENST00000658752.1:n.89+76650A>G

Variant summary

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

The ENST00000658752.1(ENSG00000248551):​n.89+76650A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 152,154 control chromosomes in the GnomAD database, including 54,179 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 0.84 (54179 hom., cov: 31)
• Consequence: ENSG00000248551 ENST00000658752.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• 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=-1.02).
• 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.89+76650A>G		intron_variant	Intron 1 of 1
ENSG00000248551	ENST00000798560.1	n.348+76650A>G		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127461 AN: 152036 Hom.: 54146 Cov.: 31

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.838 AC: 127550 AN: 152154 Hom.: 54179 Cov.: 31 AF XY: 0.831 AC XY: 61815 AN XY: 74398

African (AFR) AF: 0.772 AC: 32033 AN: 41496

American (AMR) AF: 0.861 AC: 13159 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3081 AN: 3470

East Asian (EAS) AF: 0.433 AC: 2226 AN: 5144

South Asian (SAS) AF: 0.661 AC: 3187 AN: 4818

European-Finnish (FIN) AF: 0.898 AC: 9531 AN: 10612

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.904 AC: 61477 AN: 68012

Other (OTH) AF: 0.855 AC: 1805 AN: 2112

Alfa AF: 0.867 Hom.: 9994

Bravo AF: 0.833

Asia WGS AF: 0.585 AC: 2038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.32
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs330504; hg19: chr4-176081082;