3-149054135-A-G

Position:

• chr3-149054135-A-G

Variant summary

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

The NM_003071.4(HLTF):​c.1473+1168T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 152,044 control chromosomes in the GnomAD database, including 42,634 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 0.74 (42634 hom., cov: 32)
• Consequence: HLTF NM_003071.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115

Genes affected

HLTF (HGNC:11099): (helicase like transcription factor) This gene encodes a member of the SWI/SNF family. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein contains a RING finger DNA binding motif. Two transcript variants encoding the same protein have been found for this gene. However, use of an alternative translation start site produces an isoform that is truncated at the N-terminus compared to the full-length protein. [provided by RefSeq, Jul 2008]

HLTF (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HLTF	NM_003071.4	c.1473+1168T>C		intron_variant		ENST00000310053.10	NP_003062.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLTF	ENST00000310053.10	c.1473+1168T>C		intron_variant		1	NM_003071.4	ENSP00000308944.5

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113164 AN: 151926 Hom.: 42586 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.834

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.745 AC: 113272 AN: 152044 Hom.: 42634 Cov.: 32 AF XY: 0.741 AC XY: 55112 AN XY: 74330

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.777

Alfa AF: 0.704 Hom.: 17238

Bravo AF: 0.762

Asia WGS AF: 0.673 AC: 2336 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.6
DANN	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2034906; hg19: chr3-148771922;