rs10495355

chr1-234882459-C-T

Variant summary

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

The ENST00000651370.1(ENSG00000286263):n.185+50010G>A 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 0.238 in 152,072 control chromosomes in the GnomAD database, including 5,018 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 0.24 (5018 hom., cov: 32)
• Consequence: ENST00000651370.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651370.1	n.185+50010G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36168 AN: 151954 Hom.: 5009 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.238 AC: 36206 AN: 152072 Hom.: 5018 Cov.: 32 AF XY: 0.244 AC XY: 18142 AN XY: 74344

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.268

Alfa AF: 0.197 Hom.: 4347

Bravo AF: 0.258

Asia WGS AF: 0.434 AC: 1511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	3.7
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495355; hg19: chr1-235018206;