10-32109967-T-C

Variant names:

• chr10-32109967-T-C
• rs211424
• ENST00000435436.1:n.107T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000235113 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435436.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000235113	ENST00000435436.1	TSL:6	n.107T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000301470	ENST00000779031.1		n.151T>C		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000301470	ENST00000779032.1		n.-137T>C		upstream_gene	N/A

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

African (AFR) AF: 0.620 AC: 10712 AN: 17264

American (AMR) AF: 0.840 AC: 26284 AN: 31288

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 16171 AN: 17678

East Asian (EAS) AF: 0.984 AC: 32081 AN: 32618

South Asian (SAS) AF: 0.897 AC: 52770 AN: 58860

European-Finnish (FIN) AF: 0.949 AC: 31089 AN: 32762

Middle Eastern (MID) AF: 0.851 AC: 2345 AN: 2756

European-Non Finnish (NFE) AF: 0.900 AC: 380688 AN: 422806

Other (OTH) AF: 0.881 AC: 29055 AN: 32986

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

African (AFR) AF: 0.618 AC: 25651 AN: 41500

American (AMR) AF: 0.850 AC: 13000 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3174 AN: 3472

East Asian (EAS) AF: 0.989 AC: 5118 AN: 5176

South Asian (SAS) AF: 0.907 AC: 4372 AN: 4822

European-Finnish (FIN) AF: 0.955 AC: 10140 AN: 10616

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 61157 AN: 68024

Other (OTH) AF: 0.841 AC: 1780 AN: 2116

Alfa AF: 0.853 Hom.: 28669

Bravo AF: 0.806

Asia WGS AF: 0.902 AC: 3137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.8
DANN	Benign	0.26
PhyloP100		-0.0010

Splicing

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

Other links and lift over

dbSNP: rs211424; hg19: chr10-32398895;