17-36869832-G-T

Position:

• chr17-36869832-G-T

Variant summary

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

The ENST00000616341.1(LHX1-DT):​n.99-6713C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0663 in 152,184 control chromosomes in the GnomAD database, including 452 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 0.066 (452 hom., cov: 32)
• Consequence: LHX1-DT ENST00000616341.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469

Genes affected

LHX1-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LHX1-DT	NR_135671.1	n.99-6713C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LHX1-DT	ENST00000616341.1	n.99-6713C>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0663 AC: 10088 AN: 152066 Hom.: 453 Cov.: 32

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0646

Gnomad ASJ AF: 0.0674

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0662

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0921

Gnomad OTH AF: 0.0512

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

GnomAD4 genome AF: 0.0663 AC: 10089 AN: 152184 Hom.: 452 Cov.: 32 AF XY: 0.0668 AC XY: 4968 AN XY: 74398

Gnomad4 AFR AF: 0.0165

Gnomad4 AMR AF: 0.0645

Gnomad4 ASJ AF: 0.0674

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0663

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.0922

Gnomad4 OTH AF: 0.0507

Alfa AF: 0.0829 Hom.: 410

Bravo AF: 0.0588

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17565060; hg19: chr17-35227061;