rs10517004

Variant names:

• chr4-23074916-A-G
• rs10517004
• ENST00000652324.1:n.302-8781A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652324.1(ENSG00000248837):​n.302-8781A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0451 in 152,246 control chromosomes in the GnomAD database, including 435 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 0.045 (435 hom., cov: 32)
• Consequence: ENSG00000248837 ENST00000652324.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356

Genes affected

ENSG00000248837 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374524	XR_007058432.1	n.305-8781A>G		intron_variant	Intron 3 of 7
LOC105374524	XR_007058433.1	n.305-8781A>G		intron_variant	Intron 3 of 7
LOC105374524	XR_007058434.1	n.305-8781A>G		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248837	ENST00000652324.1	n.302-8781A>G		intron_variant	Intron 3 of 9
ENSG00000248837	ENST00000653008.1	n.432-8781A>G		intron_variant	Intron 5 of 9
ENSG00000248837	ENST00000653188.1	n.331-8781A>G		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.0451 AC: 6860 AN: 152128 Hom.: 436 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0204

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.0143

Gnomad SAS AF: 0.0249

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00570

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0451 AC: 6872 AN: 152246 Hom.: 435 Cov.: 32 AF XY: 0.0440 AC XY: 3275 AN XY: 74444

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.0204

Gnomad4 ASJ AF: 0.0109

Gnomad4 EAS AF: 0.0143

Gnomad4 SAS AF: 0.0249

Gnomad4 FIN AF: 0.000188

Gnomad4 NFE AF: 0.00569

Gnomad4 OTH AF: 0.0350

Alfa AF: 0.0268 Hom.: 32

Bravo AF: 0.0492

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.36
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517004; hg19: chr4-23076539;