4-10117121-G-T

Position:

• chr4-10117121-G-T

Variant summary

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

The ENST00000701208.1(ENSG00000289865):​n.33G>T 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 0.649 in 151,982 control chromosomes in the GnomAD database, including 32,639 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 0.65 (32639 hom., cov: 32)
• Consequence: ENSG00000289865 ENST00000701208.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

Genes affected

ENSG00000289865 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900666	XR_007058030.1	n.33G>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289865	ENST00000701208.1	n.33G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98598 AN: 151866 Hom.: 32617 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.649 AC: 98676 AN: 151982 Hom.: 32639 Cov.: 32 AF XY: 0.650 AC XY: 48277 AN XY: 74272

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.681

Alfa AF: 0.582 Hom.: 1688

Bravo AF: 0.653

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.060
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3822259; hg19: chr4-10118745;