rs589249

chr1-36696751-A-Gchr1-36696751-A-T

Variant summary

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

The XR_001737977.2(LOC107984941):n.106+5465T>C 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 0.488 in 152,104 control chromosomes in the GnomAD database, including 21,612 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 0.49 (21612 hom., cov: 32)
• Consequence: LOC107984941 XR_001737977.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152

Genes affected

LOC107984941 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984941	XR_001737977.2	n.106+5465T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.487 AC: 74063 AN: 151986 Hom.: 21563 Cov.: 32

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.488 AC: 74164 AN: 152104 Hom.: 21612 Cov.: 32 AF XY: 0.488 AC XY: 36239 AN XY: 74336

Gnomad4 AFR AF: 0.814

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.473

Alfa AF: 0.305 Hom.: 1959

Bravo AF: 0.515

Asia WGS AF: 0.561 AC: 1954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	7.1
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs589249; hg19: chr1-37162352;