rs2355865

Positions:

• chr1-231458051-T-G

Variant summary

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

The ENST00000662216.1(ENSG00000287856):​c.30+4387A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,016 control chromosomes in the GnomAD database, including 9,252 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 0.32 (9252 hom., cov: 32)
• Consequence: ENSG00000287856 ENST00000662216.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

Genes affected

ENSG00000287856 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.231458051T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287856	ENST00000662216.1	c.30+4387A>C		intron_variant				ENSP00000499467.1
ENSG00000287856	ENST00000653908.1	c.30+4387A>C		intron_variant				ENSP00000499669.1
ENSG00000287856	ENST00000653198.1	n.433+4421A>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48755 AN: 151898 Hom.: 9221 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0361

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.321 AC: 48834 AN: 152016 Hom.: 9252 Cov.: 32 AF XY: 0.310 AC XY: 23030 AN XY: 74304

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.0360

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.291

Alfa AF: 0.308 Hom.: 1334

Bravo AF: 0.347

Asia WGS AF: 0.113 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2355865; hg19: chr1-231593797;