rs10516573

Variant names:

• chr4-111739881-G-A
• rs10516573
• ENST00000681719.1:n.*10G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-111739881-G-A
• chr4-111739881-G-C

Variant summary

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

The ENST00000681719.1(ENSG00000248656):​n.*10G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0646 in 152,096 control chromosomes in the GnomAD database, including 483 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 0.065 (483 hom., cov: 32)
• Consequence: ENSG00000248656 ENST00000681719.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.715

Genes affected

ENSG00000248656 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.128 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
ENSG00000248656	ENST00000681719.1	n.*10G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0643 AC: 9773 AN: 151978 Hom.: 475 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0866

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.0933

Gnomad SAS AF: 0.00767

Gnomad FIN AF: 0.0379

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0288

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0646 AC: 9821 AN: 152096 Hom.: 483 Cov.: 32 AF XY: 0.0650 AC XY: 4831 AN XY: 74330

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.0866

Gnomad4 ASJ AF: 0.00980

Gnomad4 EAS AF: 0.0935

Gnomad4 SAS AF: 0.00747

Gnomad4 FIN AF: 0.0379

Gnomad4 NFE AF: 0.0288

Gnomad4 OTH AF: 0.0620

Alfa AF: 0.0491 Hom.: 56

Bravo AF: 0.0741

Asia WGS AF: 0.0680 AC: 234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516573; hg19: chr4-112661037;