rs4652492

Positions:

• chr1-180249307-A-G
• chr1-180249307-A-T

Variant summary

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

The NM_033343.4(LHX4):​c.248+851A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,094 control chromosomes in the GnomAD database, including 19,575 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 0.50 (19575 hom., cov: 33)
• Consequence: LHX4 NM_033343.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

Genes affected

LHX4 (HGNC:21734): (LIM homeobox 4) This gene encodes a member of a large protein family which contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor involved in the control of differentiation and development of the pituitary gland. Mutations in this gene cause combined pituitary hormone deficiency 4. [provided by RefSeq, Dec 2010]

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 (SAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LHX4	NM_033343.4	c.248+851A>G		intron_variant		ENST00000263726.4	NP_203129.1
LHX4	XM_011510105.3	c.65+851A>G		intron_variant			XP_011508407.1
LHX4	XM_011510106.4	c.65+851A>G		intron_variant			XP_011508408.1
LHX4	XM_011510108.3	c.-29+851A>G		intron_variant			XP_011508410.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LHX4	ENST00000263726.4	c.248+851A>G		intron_variant		1	NM_033343.4	ENSP00000263726	P1
LHX4	ENST00000561113.1	c.185+838A>G		intron_variant, NMD_transcript_variant		2		ENSP00000452783

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76705 AN: 151974 Hom.: 19540 Cov.: 33

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.505 AC: 76799 AN: 152094 Hom.: 19575 Cov.: 33 AF XY: 0.506 AC XY: 37651 AN XY: 74346

Gnomad4 AFR AF: 0.503

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.508

Alfa AF: 0.506 Hom.: 22479

Bravo AF: 0.501

Asia WGS AF: 0.516 AC: 1794 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	9.6
DANN	Benign	0.80

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: rs4652492; hg19: chr1-180218442;