4-134766338-T-C

Variant names:

• chr4-134766338-T-C
• rs644708
• ENST00000504882.1:n.109+6831T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000249000 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.522 AC: 21594 AN: 41392

American (AMR) AF: 0.280 AC: 4256 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1314 AN: 3466

East Asian (EAS) AF: 0.175 AC: 903 AN: 5168

South Asian (SAS) AF: 0.417 AC: 2009 AN: 4814

European-Finnish (FIN) AF: 0.221 AC: 2330 AN: 10566

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19726 AN: 67806

Other (OTH) AF: 0.325 AC: 686 AN: 2112

Alfa AF: 0.309 Hom.: 30240

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
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs644708; hg19: chr4-135687493;