rs543852

Positions:

• chr2-37752757-G-A
• chr2-37752757-G-C
• chr2-37752757-G-T

Variant summary

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

The XR_001739409.2(LOC107985869):​n.234+8260G>A 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 0.53 in 151,924 control chromosomes in the GnomAD database, including 21,693 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 0.53 (21693 hom., cov: 31)
• Consequence: LOC107985869 XR_001739409.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

LOC107985869 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985869	XR_001739409.2	n.234+8260G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80409 AN: 151806 Hom.: 21676 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.530 AC: 80467 AN: 151924 Hom.: 21693 Cov.: 31 AF XY: 0.531 AC XY: 39431 AN XY: 74256

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.552

Alfa AF: 0.551 Hom.: 2642

Bravo AF: 0.515

Asia WGS AF: 0.596 AC: 2070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs543852; hg19: chr2-37979900;