4-136176485-T-C

Variant names:

• chr4-136176485-T-C
• rs1283033
• ENST00000500324.2:n.364-3125A>G

Variant summary

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

The ENST00000500324.2(ENSG00000251567):​n.364-3125A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.92 in 152,174 control chromosomes in the GnomAD database, including 65,172 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 0.92 (65172 hom., cov: 31)
• Consequence: ENSG00000251567 ENST00000500324.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519
• Publications: 0 publications found

Genes affected

ENSG00000251567 (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 (NFE) allele frequency at 95% confidence interval = 0.989 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
ENSG00000251567	ENST00000500324.2	n.364-3125A>G		intron_variant	Intron 2 of 2	3
ENSG00000251567	ENST00000513332.5	n.280-56347A>G		intron_variant	Intron 2 of 3	3
ENSG00000251567	ENST00000835416.1	n.272-3125A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.920 AC: 139875 AN: 152056 Hom.: 65117 Cov.: 31

Gnomad AFR AF: 0.781

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.969

Gnomad ASJ AF: 0.993

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.982

Gnomad FIN AF: 0.925

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.920 AC: 139990 AN: 152174 Hom.: 65172 Cov.: 31 AF XY: 0.918 AC XY: 68287 AN XY: 74402

African (AFR) AF: 0.782 AC: 32437 AN: 41494

American (AMR) AF: 0.969 AC: 14815 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.993 AC: 3446 AN: 3472

East Asian (EAS) AF: 0.745 AC: 3843 AN: 5156

South Asian (SAS) AF: 0.982 AC: 4742 AN: 4830

European-Finnish (FIN) AF: 0.925 AC: 9801 AN: 10598

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67723 AN: 68028

Other (OTH) AF: 0.942 AC: 1984 AN: 2106

Alfa AF: 0.935 Hom.: 9625

Bravo AF: 0.914

Asia WGS AF: 0.902 AC: 3139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs1283033; hg19: chr4-137097640;