rs1888732

chr1-87522158-A-G

Variant summary

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

The XR_001737795.1(LOC107985408):n.245-4282A>G variant causes a intron, non coding transcript 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: LOC107985408 XR_001737795.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611

Genes affected

LOC107985408 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107985408	XR_001737795.1	n.245-4282A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.286

Alfa AF: 0.278 Hom.: 2763

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1888732; hg19: chr1-87987841;