rs342817

chr1-229231439-G-A

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, non coding transcript 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: ENST00000651412.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651412.1	n.253-3674C>T		intron_variant, non_coding_transcript_variant

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;