ENST00000616341.1:n.98+35736G>A

Variant names:

• chr17-36900828-C-T
• rs8074144
• ENST00000616341.1:n.98+35736G>A

GermlineCancer (beta)

Variant summary

Our verdict is Benign.

<-10 Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The ENST00000616341.1(LHX1-DT):n.98+35736G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: ENST00000616341.1 is not a MANE Select or MANE Plus Clinical transcript for LHX1-DT; the reported annotation may differ from that of the MANE-designated reference transcript for this gene. The variant allele was found at a cumulative frequency of 0.189 (AC=28,772) in the gnomAD database across 152,138 control chromosomes, including 2,903 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.209. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. 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)

Classification according to ACMG Germline Pathogenicity v2019

Our verdict: Benign. The variant received -12 points.

• BP4: Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).
• BA1: GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.2087 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

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

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 4 sources Large-scale international reference populations
GnomAD3 genomes	0.189	28755	2900	152020	33
GnomAD4 genome	0.189	28772	2903	152138	33
TOPMed (Bravo)	0.184
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	0.195	41405	4194	212520
Local & regional cohorts 8 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	0.185	433	41	2342
Denmark Genome	0.257	77		300
GenomeAsia100K	0.0750	261		3478
Korea4K (4,157 Koreans)	0.00871	63		7234
Qatari Genome	0.0966	17		176
ToMMo 61KJPN (+60KJPN MNV)	0.0275	3379	54	122656
UK10K	0.210	1589		7562
WBBC (Westlake BioBank for Chinese) pilot	0.0114	102	1	8960

Showing 12 sources

Tested, but no data found:GnomAD4 exomeIf GnomAD4 is missing, the position is probably not covered by the project.

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated prediction	Prediction	Score
AlphaGenome AVI	Benign	-	2.5
BayesDel_noAF	Benign	-	-0.84
CADD	Benign	-	1.6
DANN	Benign	-	0.66
GPN-Star LLR	N/A	-	-0.55
GPN-Star score	N/A	-	0.55
PhyloP100	Benign	-	-0.33

Showing 7 of 7 scores

Other links and lift over

dbSNP: rs8074144;

hg19: chr17-35258114;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar