3-157841723-A-G

Variant names:

• chr3-157841723-A-G
• rs1399759
• ENST00000651134.1:n.1311+13911T>C

Variant summary

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

The ENST00000651134.1(ENSG00000242536):​n.1311+13911T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0583 in 152,258 control chromosomes in the GnomAD database, including 570 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 0.058 (570 hom., cov: 32)
• Consequence: ENSG00000242536 ENST00000651134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

Genes affected

ENSG00000242536 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 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
ENSG00000242536	ENST00000651134.1	n.1311+13911T>C		intron_variant	Intron 12 of 12

Frequencies

GnomAD3 genomes AF: 0.0582 AC: 8854 AN: 152140 Hom.: 566 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0465

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0437

Gnomad FIN AF: 0.000942

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0115

Gnomad OTH AF: 0.0565

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

GnomAD4 genome AF: 0.0583 AC: 8877 AN: 152258 Hom.: 570 Cov.: 32 AF XY: 0.0567 AC XY: 4219 AN XY: 74462

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.0465

Gnomad4 ASJ AF: 0.0473

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.0439

Gnomad4 FIN AF: 0.000942

Gnomad4 NFE AF: 0.0115

Gnomad4 OTH AF: 0.0649

Alfa AF: 0.0219 Hom.: 126

Bravo AF: 0.0656

Asia WGS AF: 0.130 AC: 452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.98
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1399759; hg19: chr3-157559512;