10-32109967-T-C

Variant names:

• chr10-32109967-T-C
• rs211424
• ENST00000435436.1:n.107T>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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235113	ENST00000435436.1	n.107T>C		non_coding_transcript_exon_variant	Exon 1 of 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;