rs342817

Variant names:

• chr1-229231439-G-A
• rs342817
• ENST00000651412.1:n.253-3674C>T

Variant summary

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

The ENST00000651412.1(ENSG00000233920):​n.253-3674C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,024 control chromosomes in the GnomAD database, including 19,856 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 0.49 (19856 hom., cov: 33)
• Consequence: ENSG00000233920 ENST00000651412.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

Genes affected

ENSG00000233920 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 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
ENSG00000233920	ENST00000651412.1	n.253-3674C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73862 AN: 151902 Hom.: 19804 Cov.: 33

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.487 AC: 73976 AN: 152024 Hom.: 19856 Cov.: 33 AF XY: 0.487 AC XY: 36207 AN XY: 74304

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.443

Alfa AF: 0.393 Hom.: 6764

Bravo AF: 0.508

Asia WGS AF: 0.479 AC: 1663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs342817; hg19: chr1-229367186;