rs10516573

Positions:

• 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 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.715

Genes affected

(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/exons	MANE	Protein	UniProt
		n.111739881G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;