10-32109967-T-C

Position:

• chr10-32109967-T-C

Variant summary

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

The ENST00000435436.1(ENSG00000235113):​n.107T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.882 in 801,250 control chromosomes in the GnomAD database, including 314,522 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 0.82 (53176 hom., cov: 33)
  • Exomes 𝑓: 0.90 (261346 hom.)
• Consequence: ENSG00000235113 ENST00000435436.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100

Genes affected

ENSG00000235113 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32109967T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000235113	ENST00000435436.1	n.107T>C		non_coding_transcript_exon_variant	1/2	6

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125457 AN: 152114 Hom.: 53164 Cov.: 33

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.953

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.844

GnomAD4 exome AF: 0.895 AC: 581195 AN: 649018 Hom.: 261346 Cov.: 9 AF XY: 0.897 AC XY: 306862 AN XY: 342128

Gnomad4 AFR exome AF: 0.620

Gnomad4 AMR exome AF: 0.840

Gnomad4 ASJ exome AF: 0.915

Gnomad4 EAS exome AF: 0.984

Gnomad4 SAS exome AF: 0.897

Gnomad4 FIN exome AF: 0.949

Gnomad4 NFE exome AF: 0.900

Gnomad4 OTH exome AF: 0.881

GnomAD4 genome AF: 0.824 AC: 125513 AN: 152232 Hom.: 53176 Cov.: 33 AF XY: 0.829 AC XY: 61734 AN XY: 74434

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.989

Gnomad4 SAS AF: 0.907

Gnomad4 FIN AF: 0.955

Gnomad4 NFE AF: 0.899

Gnomad4 OTH AF: 0.841

Alfa AF: 0.860 Hom.: 19219

Bravo AF: 0.806

Asia WGS AF: 0.902 AC: 3137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.8
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs211424; hg19: chr10-32398895;