rs4141232

Variant names:

• chr19-28544649-T-C
• rs4141232
• ENST00000589999.1:n.110-51626A>G

Variant summary

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

The ENST00000589999.1(ENSG00000266893):​n.110-51626A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,116 control chromosomes in the GnomAD database, including 1,772 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 0.15 (1772 hom., cov: 32)
• Consequence: ENSG00000266893 ENST00000589999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

Genes affected

ENSG00000266893 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100420587	NR_110759.1	n.657-77869A>G		intron_variant	Intron 5 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000266893	ENST00000589999.1	n.110-51626A>G		intron_variant	Intron 1 of 1	1
ENSG00000283403	ENST00000592347.5	n.643-77869A>G		intron_variant	Intron 5 of 9	1

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22184 AN: 151998 Hom.: 1773 Cov.: 32

Gnomad AFR AF: 0.0922

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.146 AC: 22187 AN: 152116 Hom.: 1772 Cov.: 32 AF XY: 0.147 AC XY: 10920 AN XY: 74378

Gnomad4 AFR AF: 0.0923

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.149

Alfa AF: 0.161 Hom.: 2905

Bravo AF: 0.144

Asia WGS AF: 0.162 AC: 560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.65
DANN	Benign	0.25
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4141232; hg19: chr19-29035556;