3-5768026-C-T

Variant names:

• chr3-5768026-C-T
• rs9311656
• ENST00000425894.2:n.461+24193C>T

Variant summary

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

The ENST00000425894.2(ENSG00000229642):​n.461+24193C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,210 control chromosomes in the GnomAD database, including 4,356 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 0.14 (4356 hom., cov: 32)
• Consequence: ENSG00000229642 ENST00000425894.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369
• Publications: 1 publications found

Genes affected

ENSG00000229642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 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
ENSG00000229642	ENST00000425894.2	n.461+24193C>T		intron_variant	Intron 3 of 8	3
ENSG00000229642	ENST00000779001.1	n.212+71540C>T		intron_variant	Intron 2 of 7
ENSG00000229642	ENST00000779002.1	n.232+71540C>T		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20779 AN: 152092 Hom.: 4334 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0594

Gnomad ASJ AF: 0.00692

Gnomad EAS AF: 0.00442

Gnomad SAS AF: 0.00372

Gnomad FIN AF: 0.00509

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.137 AC: 20858 AN: 152210 Hom.: 4356 Cov.: 32 AF XY: 0.132 AC XY: 9796 AN XY: 74428

African (AFR) AF: 0.450 AC: 18660 AN: 41464

American (AMR) AF: 0.0593 AC: 907 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00692 AC: 24 AN: 3468

East Asian (EAS) AF: 0.00443 AC: 23 AN: 5188

South Asian (SAS) AF: 0.00373 AC: 18 AN: 4830

European-Finnish (FIN) AF: 0.00509 AC: 54 AN: 10618

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0137 AC: 933 AN: 68026

Other (OTH) AF: 0.105 AC: 222 AN: 2114

Alfa AF: 0.0451 Hom.: 343

Bravo AF: 0.156

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.6
DANN	Benign	0.70
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs9311656; hg19: chr3-5809713;