4-145983152-C-T

Variant names:

• chr4-145983152-C-T
• rs11100904
• ENST00000789915.1:n.271-1523C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000789915.1(ENSG00000302837):​n.271-1523C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 149,064 control chromosomes in the GnomAD database, including 10,567 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 0.37 (10567 hom., cov: 32)
• Consequence: ENSG00000302837 ENST00000789915.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 8 publications found

Genes affected

ENSG00000302837 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 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
ENSG00000302837	ENST00000789915.1	n.271-1523C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.366 AC: 54448 AN: 148946 Hom.: 10567 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.365 AC: 54478 AN: 149064 Hom.: 10567 Cov.: 32 AF XY: 0.356 AC XY: 25960 AN XY: 72852

African (AFR) AF: 0.341 AC: 13150 AN: 38602

American (AMR) AF: 0.354 AC: 5374 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 892 AN: 3470

East Asian (EAS) AF: 0.0875 AC: 454 AN: 5190

South Asian (SAS) AF: 0.377 AC: 1819 AN: 4822

European-Finnish (FIN) AF: 0.324 AC: 3424 AN: 10556

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28197 AN: 67966

Other (OTH) AF: 0.317 AC: 663 AN: 2092

Alfa AF: 0.391 Hom.: 34428

Bravo AF: 0.356

Asia WGS AF: 0.248 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.7
DANN	Benign	0.73
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs11100904; hg19: chr4-146904304;