4-134766338-T-C

Variant names:

• chr4-134766338-T-C
• rs644708
• ENST00000504882.1:n.109+6831T>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 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: ENSG00000249000 ENST00000504882.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579

Genes affected

ENSG00000249000 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249000	ENST00000504882.1	n.109+6831T>C		intron_variant	Intron 1 of 4	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;