chr17-36906671-G-A

Variant names:

• chr17-36906671-G-A
• rs7218928
• ENST00000616341.1:n.98+29893C>T

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+29893C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 152,108 control chromosomes in the GnomAD database, including 25,749 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 0.58 (25749 hom., cov: 33)
• Consequence: LHX1-DT ENST00000616341.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 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+29893C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LHX1-DT	ENST00000616341.1	TSL:2	n.98+29893C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88162 AN: 151990 Hom.: 25735 Cov.: 33

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.580 AC: 88216 AN: 152108 Hom.: 25749 Cov.: 33 AF XY: 0.576 AC XY: 42814 AN XY: 74354

African (AFR) AF: 0.644 AC: 26738 AN: 41490

American (AMR) AF: 0.511 AC: 7807 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1796 AN: 3468

East Asian (EAS) AF: 0.485 AC: 2504 AN: 5168

South Asian (SAS) AF: 0.492 AC: 2376 AN: 4826

European-Finnish (FIN) AF: 0.529 AC: 5581 AN: 10554

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39359 AN: 67988

Other (OTH) AF: 0.563 AC: 1192 AN: 2116

Alfa AF: 0.575 Hom.: 105883

Bravo AF: 0.582

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.20
PhyloP100		-0.46

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: rs7218928;

hg19: chr17-35263956;