chr1-231433945-C-T

Variant names:

• chr1-231433945-C-T
• rs12093061
• ENST00000662216.1:c.30+28493G>A

Variant summary

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

The ENST00000662216.1(ENSG00000287856):​c.30+28493G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 152,090 control chromosomes in the GnomAD database, including 21,302 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 0.51 (21302 hom., cov: 33)
• Consequence: ENSG00000287856 ENST00000662216.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968

Genes affected

ENSG00000287856 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.716 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
ENSG00000287856	ENST00000662216.1	c.30+28493G>A		intron_variant	Intron 3 of 6			ENSP00000499467.1
ENSG00000287856	ENST00000653908.1	c.30+28493G>A		intron_variant	Intron 2 of 4			ENSP00000499669.1
ENSG00000287856	ENST00000653198.1	n.433+28527G>A		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77470 AN: 151972 Hom.: 21248 Cov.: 33

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.510 AC: 77577 AN: 152090 Hom.: 21302 Cov.: 33 AF XY: 0.503 AC XY: 37379 AN XY: 74342

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.499

Alfa AF: 0.445 Hom.: 15892

Bravo AF: 0.540

Asia WGS AF: 0.508 AC: 1771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	7.9
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12093061; hg19: chr1-231569691;