rs7218928

chr17-36906671-G-A

Variant summary

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

The NR_135671.1(LHX1-DT):n.98+29893C>T variant causes a intron, non coding transcript 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 NR_135671.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LHX1-DT	NR_135671.1	n.98+29893C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LHX1-DT	ENST00000616341.1	n.98+29893C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.563

Alfa AF: 0.573 Hom.: 46843

Bravo AF: 0.582

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7218928; hg19: chr17-35263956;