4-134766338-T-C

Position:

• chr4-134766338-T-C

Variant summary

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

The ENST00000504882.1(ENSG00000249000):​n.109+6831T>C 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 0.351 in 151,732 control chromosomes in the GnomAD database, including 10,340 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 0.35 (10340 hom., cov: 32)
• Consequence: ENST00000504882.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000504882.1	n.109+6831T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53175 AN: 151614 Hom.: 10312 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.351 AC: 53251 AN: 151732 Hom.: 10340 Cov.: 32 AF XY: 0.348 AC XY: 25816 AN XY: 74144

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.325

Alfa AF: 0.303 Hom.: 11673

Bravo AF: 0.354

Asia WGS AF: 0.286 AC: 997 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs644708; hg19: chr4-135687493;