rs2355865

Variant names:

• chr1-231458051-T-G
• rs2355865
• ENST00000662216.1:c.30+4387A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000287856 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662216.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287856	ENST00000662216.1		c.30+4387A>C		intron	N/A	ENSP00000499467.1
	ENSG00000287856	ENST00000653908.1		c.30+4387A>C		intron	N/A	ENSP00000499669.1
	ENSG00000287856	ENST00000653198.1		n.433+4421A>C		intron	N/A

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

African (AFR) AF: 0.511 AC: 21179 AN: 41412

American (AMR) AF: 0.336 AC: 5135 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 797 AN: 3466

East Asian (EAS) AF: 0.0360 AC: 187 AN: 5190

South Asian (SAS) AF: 0.120 AC: 580 AN: 4826

European-Finnish (FIN) AF: 0.183 AC: 1935 AN: 10576

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18077 AN: 67962

Other (OTH) AF: 0.291 AC: 615 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.76
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2355865; hg19: chr1-231593797;