rs1316288

Variant names:

• chr2-574307-T-C
• rs1316288
• ENST00000444079.1:n.619-3695T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-574307-T-C
• chr2-574307-T-G

Variant summary

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

The ENST00000444079.1(ENSG00000233633):​n.619-3695T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,228 control chromosomes in the GnomAD database, including 6,471 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 0.20 (6471 hom., cov: 33)
• Consequence: ENSG00000233633 ENST00000444079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

ENSG00000233633 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 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
ENSG00000233633	ENST00000444079.1	n.619-3695T>C		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31060 AN: 152110 Hom.: 6444 Cov.: 33

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0858

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.0883

Gnomad FIN AF: 0.0718

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0559

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.205 AC: 31144 AN: 152228 Hom.: 6471 Cov.: 33 AF XY: 0.203 AC XY: 15118 AN XY: 74428

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.0858

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.0886

Gnomad4 FIN AF: 0.0718

Gnomad4 NFE AF: 0.0559

Gnomad4 OTH AF: 0.168

Alfa AF: 0.0897 Hom.: 802

Bravo AF: 0.227

Asia WGS AF: 0.187 AC: 651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.27
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1316288; hg19: chr2-574307;