6-30908461-G-A

Position:

• chr6-30908461-G-A

Variant summary

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

The NM_001517.5(GTF2H4):​c.-4+58G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 167,578 control chromosomes in the GnomAD database, including 6,689 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 0.26 (6011 hom., cov: 31)
  • Exomes 𝑓: 0.24 (678 hom.)
• Consequence: GTF2H4 NM_001517.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

Genes affected

GTF2H4 (HGNC:4658): (general transcription factor IIH subunit 4) Enables RNA polymerase II general transcription initiation factor activity. Involved in transcription by RNA polymerase II. Located in nuclear speck. Part of core TFIIH complex portion of holo TFIIH complex and transcription factor TFIID complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GTF2H4	NM_001517.5	c.-4+58G>A		intron_variant		ENST00000259895.9	NP_001508.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GTF2H4	ENST00000259895.9	c.-4+58G>A		intron_variant		1	NM_001517.5	ENSP00000259895	P1
GTF2H4	ENST00000376316.5	c.-4+83G>A		intron_variant		5		ENSP00000365493	P1
GTF2H4	ENST00000453897.4	n.181+58G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39373 AN: 151734 Hom.: 5997 Cov.: 31

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.255

GnomAD4 exome AF: 0.240 AC: 3770 AN: 15724 Hom.: 678 AF XY: 0.255 AC XY: 2156 AN XY: 8468

Gnomad4 AFR exome AF: 0.179

Gnomad4 AMR exome AF: 0.410

Gnomad4 ASJ exome AF: 0.198

Gnomad4 EAS exome AF: 0.454

Gnomad4 SAS exome AF: 0.403

Gnomad4 FIN exome AF: 0.161

Gnomad4 NFE exome AF: 0.134

Gnomad4 OTH exome AF: 0.254

GnomAD4 genome AF: 0.260 AC: 39410 AN: 151854 Hom.: 6011 Cov.: 31 AF XY: 0.270 AC XY: 20019 AN XY: 74212

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.263

Alfa AF: 0.200 Hom.: 988

Bravo AF: 0.266

Asia WGS AF: 0.551 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.6
DANN	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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: rs2074509; hg19: chr6-30876238;