rs2995271

Positions:

• chr10-30230903-C-T

Variant summary

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

The NR_120653.1(LOC101929279):​n.269-14C>T 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 0.642 in 152,022 control chromosomes in the GnomAD database, including 33,695 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 0.64 (33695 hom., cov: 31)
• Consequence: LOC101929279 NR_120653.1 splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281

Genes affected

LOC101929279 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929279	NR_120653.1	n.269-14C>T		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97631 AN: 151904 Hom.: 33684 Cov.: 31

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.642 AC: 97671 AN: 152022 Hom.: 33695 Cov.: 31 AF XY: 0.643 AC XY: 47772 AN XY: 74280

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.650

Alfa AF: 0.749 Hom.: 58823

Bravo AF: 0.621

Asia WGS AF: 0.437 AC: 1522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	8.1
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2995271; hg19: chr10-30519832;