rs1316288

Positions:

• 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, non coding transcript 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: ENST00000444079.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000444079.1	n.619-3695T>C		intron_variant, non_coding_transcript_variant		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;