17-36900828-C-T

Variant names:

• chr17-36900828-C-T
• rs8074144
• ENST00000616341.1:n.98+35736G>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.98+35736G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,138 control chromosomes in the GnomAD database, including 2,903 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 0.19 (2903 hom., cov: 33)
• Consequence: LHX1-DT ENST00000616341.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331
• Publications: 5 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.209 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LHX1-DT	NR_135671.1		n.98+35736G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LHX1-DT	ENST00000616341.1	TSL:2	n.98+35736G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28755 AN: 152020 Hom.: 2900 Cov.: 33

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0131

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.189 AC: 28772 AN: 152138 Hom.: 2903 Cov.: 33 AF XY: 0.186 AC XY: 13862 AN XY: 74370

African (AFR) AF: 0.196 AC: 8116 AN: 41488

American (AMR) AF: 0.136 AC: 2072 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 571 AN: 3470

East Asian (EAS) AF: 0.0131 AC: 68 AN: 5190

South Asian (SAS) AF: 0.109 AC: 528 AN: 4822

European-Finnish (FIN) AF: 0.208 AC: 2201 AN: 10582

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14388 AN: 67988

Other (OTH) AF: 0.193 AC: 407 AN: 2110

Alfa AF: 0.196 Hom.: 3941

Bravo AF: 0.184

Asia WGS AF: 0.0750 AC: 261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.66
PhyloP100		-0.33

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs8074144;

hg19: chr17-35258114;