1-229224758-T-C

Variant names:

• chr1-229224758-T-C
• rs2988738
• ENST00000430677.1:n.303-808A>G

Variant summary

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

The ENST00000430677.1(ENSG00000233920):​n.303-808A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0385 in 152,306 control chromosomes in the GnomAD database, including 251 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 0.039 (251 hom., cov: 32)
• Consequence: ENSG00000233920 ENST00000430677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142

Genes affected

ENSG00000233920 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 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	ENST00000430677.1	n.303-808A>G		intron_variant	Intron 1 of 1	3
ENSG00000233920	ENST00000651412.1	n.428-808A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0385 AC: 5853 AN: 152188 Hom.: 248 Cov.: 32

Gnomad AFR AF: 0.0300

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0985

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0163

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0152

Gnomad OTH AF: 0.0449

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

GnomAD4 genome AF: 0.0385 AC: 5868 AN: 152306 Hom.: 251 Cov.: 32 AF XY: 0.0420 AC XY: 3125 AN XY: 74486

Gnomad4 AFR AF: 0.0303

Gnomad4 AMR AF: 0.0989

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0163

Gnomad4 NFE AF: 0.0152

Gnomad4 OTH AF: 0.0444

Alfa AF: 0.0292 Hom.: 36

Bravo AF: 0.0447

Asia WGS AF: 0.125 AC: 434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2988738; hg19: chr1-229360505;