rs10937331

Positions:

• chr3-188030289-A-G

Variant summary

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

The XR_001741061.2(LOC107986166):​n.162+11829T>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 0.342 in 152,028 control chromosomes in the GnomAD database, including 9,577 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 0.34 (9577 hom., cov: 31)
• Consequence: LOC107986166 XR_001741061.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500

Genes affected

LOC107986166 (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 = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986166	XR_001741061.2	n.162+11829T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51992 AN: 151910 Hom.: 9572 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.342 AC: 52014 AN: 152028 Hom.: 9577 Cov.: 31 AF XY: 0.340 AC XY: 25295 AN XY: 74294

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.374

Alfa AF: 0.372 Hom.: 1878

Bravo AF: 0.336

Asia WGS AF: 0.214 AC: 750 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	2.2
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10937331; hg19: chr3-187748077;