7-1234209-A-T

Position:

• chr7-1234209-A-T

Variant summary

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

The NM_001080461.3(UNCX):​c.450+514A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,230 control chromosomes in the GnomAD database, including 32,949 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 0.61 (32949 hom., cov: 33)
• Consequence: UNCX NM_001080461.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650

Genes affected

UNCX (HGNC:33194): (UNC homeobox) This gene encodes a homeobox transcription factor that is involved in somitogenesis and neurogenesis and is required for the maintenance and differentiation of specific elements of the axial skeleton. This gene also plays a role in controlling the development of connections of hypothalamic neurons to pituitary elements, allowing central neurons to reach the peripheral blood circulation and deliver hormones that control peripheral functions. The expression of this gene is associated with an increased frequency of acute myeloid leukemia. [provided by RefSeq, Jul 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UNCX	NM_001080461.3	c.450+514A>T		intron_variant		ENST00000316333.9	NP_001073930.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UNCX	ENST00000316333.9	c.450+514A>T		intron_variant		1	NM_001080461.3	ENSP00000314480	P1

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92341 AN: 152112 Hom.: 32944 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.607 AC: 92355 AN: 152230 Hom.: 32949 Cov.: 33 AF XY: 0.607 AC XY: 45154 AN XY: 74440

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.702

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.800

Gnomad4 OTH AF: 0.608

Alfa AF: 0.619 Hom.: 2432

Bravo AF: 0.581

Asia WGS AF: 0.546 AC: 1903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	14
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10275044; hg19: chr7-1273845;