ENST00000503017.2:n.332+13838A>G

Variant names:

• chr4-23017081-A-G
• rs7664442
• ENST00000503017.2:n.332+13838A>G

Variant summary

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

The ENST00000503017.2(ENSG00000248837):​n.332+13838A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0802 in 152,116 control chromosomes in the GnomAD database, including 530 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 0.080 (530 hom., cov: 32)
• Consequence: ENSG00000248837 ENST00000503017.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391
• Publications: 4 publications found

Genes affected

ENSG00000248837 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.088 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503017.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248837	ENST00000503017.2	TSL:2	n.332+13838A>G		intron	N/A
	ENSG00000248837	ENST00000506425.2	TSL:3	n.304+13838A>G		intron	N/A
	ENSG00000248837	ENST00000511453.5	TSL:3	n.285+13838A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0802 AC: 12191 AN: 152002 Hom.: 525 Cov.: 32

Gnomad AFR AF: 0.0902

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.0546

Gnomad ASJ AF: 0.0673

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.0406

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0768

Gnomad OTH AF: 0.0840

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

GnomAD4 genome AF: 0.0802 AC: 12206 AN: 152116 Hom.: 530 Cov.: 32 AF XY: 0.0806 AC XY: 5992 AN XY: 74376

African (AFR) AF: 0.0904 AC: 3753 AN: 41502

American (AMR) AF: 0.0545 AC: 833 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0673 AC: 233 AN: 3464

East Asian (EAS) AF: 0.0522 AC: 270 AN: 5168

South Asian (SAS) AF: 0.0402 AC: 194 AN: 4822

European-Finnish (FIN) AF: 0.128 AC: 1349 AN: 10558

Middle Eastern (MID) AF: 0.107 AC: 31 AN: 290

European-Non Finnish (NFE) AF: 0.0768 AC: 5223 AN: 67996

Other (OTH) AF: 0.0841 AC: 178 AN: 2116

Alfa AF: 0.0755 Hom.: 792

Bravo AF: 0.0771

Asia WGS AF: 0.0600 AC: 205 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.79
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs7664442; hg19: chr4-23018704;