rs1464311

Variant names:

• chr3-118482382-T-C
• rs1464311
• ENST00000482142.5:n.232+14241A>G

Variant summary

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

The ENST00000482142.5(ENSG00000243276):​n.232+14241A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 151,572 control chromosomes in the GnomAD database, including 1,223 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 0.12 (1223 hom., cov: 33)
• Consequence: ENSG00000243276 ENST00000482142.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 4 publications found

Genes affected

ENSG00000243276 (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 = 0.138 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
ENSG00000243276	ENST00000482142.5	n.232+14241A>G		intron_variant	Intron 3 of 6	5
ENSG00000243276	ENST00000833975.1	n.448+14241A>G		intron_variant	Intron 5 of 5
ENSG00000243276	ENST00000833976.1	n.349+14241A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18380 AN: 151454 Hom.: 1222 Cov.: 33

Gnomad AFR AF: 0.0881

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0828

Gnomad EAS AF: 0.0242

Gnomad SAS AF: 0.0840

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.121 AC: 18390 AN: 151572 Hom.: 1223 Cov.: 33 AF XY: 0.123 AC XY: 9130 AN XY: 74142

African (AFR) AF: 0.0881 AC: 3624 AN: 41156

American (AMR) AF: 0.105 AC: 1595 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0828 AC: 287 AN: 3468

East Asian (EAS) AF: 0.0241 AC: 125 AN: 5190

South Asian (SAS) AF: 0.0843 AC: 407 AN: 4830

European-Finnish (FIN) AF: 0.218 AC: 2298 AN: 10558

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9551 AN: 67822

Other (OTH) AF: 0.120 AC: 252 AN: 2106

Alfa AF: 0.130 Hom.: 2338

Bravo AF: 0.111

Asia WGS AF: 0.0680 AC: 236 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.40
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1464311; hg19: chr3-118201229;