rs952153

Positions:

• chr10-2563132-C-A
• chr10-2563132-C-G
• chr10-2563132-C-T

Variant summary

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

The NR_188171.1(LOC105376350):​n.254+3125C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,032 control chromosomes in the GnomAD database, including 41,023 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 0.72 (41023 hom., cov: 32)
• Consequence: LOC105376350 NR_188171.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277

Genes affected

ENSG00000235281 (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 = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376350	NR_188171.1	n.254+3125C>A		intron_variant
LOC105376350	NR_188172.1	n.138-3397C>A		intron_variant
LOC105376350	NR_188173.1	n.138-7064C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000235281	ENST00000438753.1	n.208-3397C>A		intron_variant		5
ENSG00000235281	ENST00000656735.1	n.481+3125C>A		intron_variant
ENSG00000235281	ENST00000656797.1	n.115-52357C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109633 AN: 151916 Hom.: 41001 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.721 AC: 109682 AN: 152032 Hom.: 41023 Cov.: 32 AF XY: 0.719 AC XY: 53464 AN XY: 74314

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.762

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.729

Alfa AF: 0.731 Hom.: 2508

Bravo AF: 0.696

Asia WGS AF: 0.600 AC: 2091 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	0.77
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs952153; hg19: chr10-2605324;