chr4-162775233-C-T

Variant names:

• chr4-162775233-C-T
• rs1458152
• ENST00000661387.1:n.165+33454C>T

Variant summary

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

The ENST00000661387.1(ENSG00000248431):​n.165+33454C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.957 in 152,156 control chromosomes in the GnomAD database, including 69,774 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 0.96 (69774 hom., cov: 32)
• Consequence: ENSG00000248431 ENST00000661387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199
• Publications: 0 publications found

Genes affected

ENSG00000248431 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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
ENSG00000248431	ENST00000661387.1	n.165+33454C>T		intron_variant	Intron 2 of 3
ENSG00000248431	ENST00000728266.1	n.185+33454C>T		intron_variant	Intron 2 of 6
ENSG00000248431	ENST00000728267.1	n.536-10032C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.957 AC: 145541 AN: 152038 Hom.: 69740 Cov.: 32

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.998

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.965

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

GnomAD4 genome AF: 0.957 AC: 145629 AN: 152156 Hom.: 69774 Cov.: 32 AF XY: 0.959 AC XY: 71345 AN XY: 74404

African (AFR) AF: 0.911 AC: 37874 AN: 41554

American (AMR) AF: 0.970 AC: 14787 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.998 AC: 3463 AN: 3470

East Asian (EAS) AF: 0.993 AC: 5141 AN: 5176

South Asian (SAS) AF: 0.977 AC: 4721 AN: 4830

European-Finnish (FIN) AF: 0.978 AC: 10382 AN: 10616

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.972 AC: 66024 AN: 67946

Other (OTH) AF: 0.965 AC: 2037 AN: 2110

Alfa AF: 0.964 Hom.: 9147

Bravo AF: 0.956

Asia WGS AF: 0.964 AC: 3349 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.49
DANN	Benign	0.44
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1458152; hg19: chr4-163696385;