4-111739881-G-A

Variant names:

• chr4-111739881-G-A
• rs10516573
• ENST00000751011.1:n.126-24559C>T

Variant summary

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

The ENST00000751011.1(ENSG00000297804):​n.126-24559C>T variant causes a intron 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: ENSG00000297804 ENST00000751011.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.715
• Publications: 2 publications found

Genes affected

ENSG00000297804 (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 = 0.128 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751011.1. 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
	ENSG00000297804	ENST00000751011.1		n.126-24559C>T		intron	N/A
	ENSG00000297804	ENST00000751012.1		n.90-24559C>T		intron	N/A
	ENSG00000248656	ENST00000681719.1		n.*10G>A		downstream_gene	N/A

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

African (AFR) AF: 0.131 AC: 5433 AN: 41474

American (AMR) AF: 0.0866 AC: 1322 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.00980 AC: 34 AN: 3470

East Asian (EAS) AF: 0.0935 AC: 483 AN: 5164

South Asian (SAS) AF: 0.00747 AC: 36 AN: 4820

European-Finnish (FIN) AF: 0.0379 AC: 401 AN: 10578

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0288 AC: 1958 AN: 68010

Other (OTH) AF: 0.0620 AC: 131 AN: 2114

Alfa AF: 0.0402 Hom.: 300

Bravo AF: 0.0741

Asia WGS AF: 0.0680 AC: 234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.7
DANN	Benign	0.73
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs10516573; hg19: chr4-112661037;