5-163225545-C-T

Variant names:

• chr5-163225545-C-T
• rs4448013
• ENST00000503504.2:n.512+31306G>A

Variant summary

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

The ENST00000509211.2(ENSG00000254186):​n.527+31306G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,840 control chromosomes in the GnomAD database, including 16,519 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 0.39 (16519 hom., cov: 32)
• Consequence: ENSG00000254186 ENST00000509211.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 2 publications found

Genes affected

ENSG00000254186 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509211.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254186	ENST00000503504.2	TSL:5	n.512+31306G>A		intron	N/A
	ENSG00000254186	ENST00000509211.2	TSL:3	n.527+31306G>A		intron	N/A
	ENSG00000254186	ENST00000646617.1		n.323-136199G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59006 AN: 151722 Hom.: 16482 Cov.: 32

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.389 AC: 59097 AN: 151840 Hom.: 16519 Cov.: 32 AF XY: 0.388 AC XY: 28776 AN XY: 74216

African (AFR) AF: 0.787 AC: 32614 AN: 41448

American (AMR) AF: 0.300 AC: 4578 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3468

East Asian (EAS) AF: 0.461 AC: 2377 AN: 5158

South Asian (SAS) AF: 0.403 AC: 1943 AN: 4818

European-Finnish (FIN) AF: 0.187 AC: 1963 AN: 10492

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.202 AC: 13694 AN: 67900

Other (OTH) AF: 0.371 AC: 780 AN: 2102

Alfa AF: 0.224 Hom.: 4750

Bravo AF: 0.414

Asia WGS AF: 0.437 AC: 1519 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.22
PhyloP100		-0.63

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4448013;

hg19: chr5-162652551;