rs1567804

chr2-100727176-A-G

Variant summary

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

The XR_001739612.2(LOC105375310):n.2416-2820T>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 0.549 in 152,114 control chromosomes in the GnomAD database, including 25,287 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 0.55 (25287 hom., cov: 33)
• Consequence: LOC105375310 XR_001739612.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353

Genes affected

LOC105375310 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375310	XR_001739612.2	n.2416-2820T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83446 AN: 151996 Hom.: 25289 Cov.: 33

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.549 AC: 83457 AN: 152114 Hom.: 25287 Cov.: 33 AF XY: 0.546 AC XY: 40576 AN XY: 74368

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.684

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.555

Alfa AF: 0.654 Hom.: 62812

Bravo AF: 0.520

Asia WGS AF: 0.330 AC: 1147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.7
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1567804; hg19: chr2-101343638;