rs17565060

Variant names:

• chr17-36869832-G-T
• rs17565060
• ENST00000616341.1:n.99-6713C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

LHX1-DT (HGNC:53778): (LHX1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000616341.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LHX1-DT	NR_135671.1		n.99-6713C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LHX1-DT	ENST00000616341.1	TSL:2	n.99-6713C>A		intron	N/A

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

African (AFR) AF: 0.0165 AC: 685 AN: 41538

American (AMR) AF: 0.0645 AC: 987 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0674 AC: 234 AN: 3472

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5182

South Asian (SAS) AF: 0.0663 AC: 319 AN: 4814

European-Finnish (FIN) AF: 0.136 AC: 1439 AN: 10582

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0922 AC: 6268 AN: 67986

Other (OTH) AF: 0.0507 AC: 107 AN: 2112

Alfa AF: 0.0816 Hom.: 481

Bravo AF: 0.0588

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.87
PhyloP100		0.47
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17565060; hg19: chr17-35227061;