4-90102161-C-T

Variant names:

• chr4-90102161-C-T
• rs1838227
• ENST00000740240.1:n.114+16380G>A

Variant summary

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

The ENST00000740240.1(ENSG00000296542):​n.114+16380G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 151,438 control chromosomes in the GnomAD database, including 8,247 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 0.31 (8247 hom., cov: 32)
• Consequence: ENSG00000296542 ENST00000740240.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 3 publications found

Genes affected

ENSG00000296542 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 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
ENSG00000296542	ENST00000740240.1	n.114+16380G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46624 AN: 151318 Hom.: 8250 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.308 AC: 46620 AN: 151438 Hom.: 8247 Cov.: 32 AF XY: 0.308 AC XY: 22773 AN XY: 73958

African (AFR) AF: 0.146 AC: 6030 AN: 41348

American (AMR) AF: 0.276 AC: 4190 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 922 AN: 3464

East Asian (EAS) AF: 0.204 AC: 1044 AN: 5124

South Asian (SAS) AF: 0.270 AC: 1300 AN: 4812

European-Finnish (FIN) AF: 0.443 AC: 4642 AN: 10478

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27528 AN: 67736

Other (OTH) AF: 0.285 AC: 599 AN: 2100

Alfa AF: 0.367 Hom.: 2345

Bravo AF: 0.288

Asia WGS AF: 0.232 AC: 797 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.82
DANN	Benign	0.17
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1838227; hg19: chr4-91023312;