5-33053330-T-C

Variant names:

• chr5-33053330-T-C
• rs4049377
• ENST00000510327.2:n.503-30003A>G

Variant summary

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

The ENST00000510327.2(ENSG00000250697):​n.503-30003A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.937 in 151,980 control chromosomes in the GnomAD database, including 66,817 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 0.94 (66817 hom., cov: 30)
• Consequence: ENSG00000250697 ENST00000510327.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 1 publications found

Genes affected

ENSG00000250697 (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 (AFR) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510327.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250697	ENST00000510327.2	TSL:3	n.503-30003A>G		intron	N/A
	ENSG00000250697	ENST00000657441.1		n.270-30003A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.937 AC: 142285 AN: 151862 Hom.: 66763 Cov.: 30

Gnomad AFR AF: 0.976

Gnomad AMI AF: 0.892

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.920

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

GnomAD4 genome AF: 0.937 AC: 142396 AN: 151980 Hom.: 66817 Cov.: 30 AF XY: 0.934 AC XY: 69363 AN XY: 74290

African (AFR) AF: 0.976 AC: 40576 AN: 41558

American (AMR) AF: 0.873 AC: 13325 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.932 AC: 3233 AN: 3470

East Asian (EAS) AF: 0.846 AC: 4363 AN: 5160

South Asian (SAS) AF: 0.938 AC: 4519 AN: 4820

European-Finnish (FIN) AF: 0.902 AC: 9488 AN: 10524

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.941 AC: 63868 AN: 67886

Other (OTH) AF: 0.920 AC: 1932 AN: 2100

Alfa AF: 0.942 Hom.: 8212

Bravo AF: 0.933

Asia WGS AF: 0.904 AC: 3128 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.41
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs4049377; hg19: chr5-33053436;