rs1888732

Variant names:

• chr1-87522158-A-G
• rs1888732
• ENST00000755956.1:n.679-4282A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000755956.1(ENSG00000298492):​n.679-4282A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,034 control chromosomes in the GnomAD database, including 6,616 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 0.29 (6616 hom., cov: 32)
• Consequence: ENSG00000298492 ENST00000755956.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611
• Publications: 1 publications found

Genes affected

ENSG00000298492 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985408	XR_001737795.1	n.245-4282A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298492	ENST00000755956.1	n.679-4282A>G		intron_variant	Intron 4 of 7
ENSG00000298492	ENST00000755957.1	n.245-4282A>G		intron_variant	Intron 1 of 3
ENSG00000298492	ENST00000755958.1	n.405-4282A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43754 AN: 151916 Hom.: 6591 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.288 AC: 43829 AN: 152034 Hom.: 6616 Cov.: 32 AF XY: 0.286 AC XY: 21235 AN XY: 74316

African (AFR) AF: 0.371 AC: 15381 AN: 41440

American (AMR) AF: 0.282 AC: 4311 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1074 AN: 3468

East Asian (EAS) AF: 0.122 AC: 630 AN: 5170

South Asian (SAS) AF: 0.315 AC: 1518 AN: 4826

European-Finnish (FIN) AF: 0.193 AC: 2043 AN: 10586

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.264 AC: 17914 AN: 67960

Other (OTH) AF: 0.286 AC: 603 AN: 2110

Alfa AF: 0.279 Hom.: 3154

Bravo AF: 0.298

Asia WGS AF: 0.214 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.78
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs1888732; hg19: chr1-87987841;