rs10937329

chr3-187995930-T-Achr3-187995930-T-G

Variant summary

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

The XR_001741061.2(LOC107986166):n.2244A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 151,968 control chromosomes in the GnomAD database, including 6,104 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 0.27 (6104 hom., cov: 32)
• Consequence: LOC107986166 XR_001741061.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285

Genes affected

LOC107986166 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986166	XR_001741061.2	n.2244A>T		non_coding_transcript_exon_variant	5/5
LOC107986166	XR_001741062.2	n.2145A>T		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41514 AN: 151850 Hom.: 6098 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.273 AC: 41539 AN: 151968 Hom.: 6104 Cov.: 32 AF XY: 0.275 AC XY: 20436 AN XY: 74252

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.305

Alfa AF: 0.312 Hom.: 4132

Bravo AF: 0.267

Asia WGS AF: 0.289 AC: 1006 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.4
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10937329; hg19: chr3-187713718; COSMIC: COSV68817889;