chr3-67310-A-G

Position:

• chr3-67310-A-G

Variant summary

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

The XR_940533.2(LOC105376921):​n.124-15A>G variant causes a splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 151,928 control chromosomes in the GnomAD database, including 4,118 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 0.22 (4118 hom., cov: 31)
• Consequence: LOC105376921 XR_940533.2 splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503

Genes affected

LOC105376921 (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 (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376921	XR_940533.2	n.124-15A>G		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33501 AN: 151810 Hom.: 4115 Cov.: 31

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.221 AC: 33526 AN: 151928 Hom.: 4118 Cov.: 31 AF XY: 0.225 AC XY: 16694 AN XY: 74224

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.219

Alfa AF: 0.175 Hom.: 3045

Bravo AF: 0.228

Asia WGS AF: 0.372 AC: 1291 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	0.43
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: rs9841287; hg19: chr3-108993;