rs4750727

Positions:

• chr10-129035457-A-G

Variant summary

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

The ENST00000685374.2(ENSG00000289400):​n.1112T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0787 in 152,306 control chromosomes in the GnomAD database, including 1,027 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 0.079 (1027 hom., cov: 33)
• Consequence: ENST00000685374.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.471

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902559	XR_007062390.1	n.1108T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000685374.2	n.1112T>C		non_coding_transcript_exon_variant	2/2
	ENST00000688275.1	n.786T>C		non_coding_transcript_exon_variant	3/3
	ENST00000689194.1	n.1173T>C		non_coding_transcript_exon_variant	2/2
	ENST00000701287.1	n.1282T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0785 AC: 11947 AN: 152188 Hom.: 1017 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0478

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0148

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0626

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

GnomAD4 genome AF: 0.0787 AC: 11992 AN: 152306 Hom.: 1027 Cov.: 33 AF XY: 0.0774 AC XY: 5762 AN XY: 74488

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.0478

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.0172

Gnomad4 FIN AF: 0.0148

Gnomad4 NFE AF: 0.0202

Gnomad4 OTH AF: 0.0619

Alfa AF: 0.0613 Hom.: 107

Bravo AF: 0.0879

Asia WGS AF: 0.0700 AC: 244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.37
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4750727; hg19: chr10-130833721;