10-8400893-C-T

Variant names:

• chr10-8400893-C-T
• rs2787140
• ENST00000413286.1:n.34C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000413286.1(ENSG00000226990):​n.34C>T 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 0.06 in 152,232 control chromosomes in the GnomAD database, including 368 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 0.060 (368 hom., cov: 32)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: ENSG00000226990 ENST00000413286.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 1 publications found

Genes affected

ENSG00000226990 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0835 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413286.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226990	ENST00000413286.1	TSL:3	n.34C>T		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000226990	ENST00000798213.1		n.113C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000226990	ENST00000798205.1		n.629-481C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0600 AC: 9124 AN: 152108 Hom.: 369 Cov.: 32

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.0567

Gnomad ASJ AF: 0.0675

Gnomad EAS AF: 0.0855

Gnomad SAS AF: 0.0460

Gnomad FIN AF: 0.0576

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0853

Gnomad OTH AF: 0.0478

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 1 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0600 AC: 9129 AN: 152226 Hom.: 368 Cov.: 32 AF XY: 0.0597 AC XY: 4441 AN XY: 74434

African (AFR) AF: 0.0160 AC: 663 AN: 41550

American (AMR) AF: 0.0567 AC: 866 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0675 AC: 234 AN: 3468

East Asian (EAS) AF: 0.0857 AC: 444 AN: 5182

South Asian (SAS) AF: 0.0460 AC: 222 AN: 4826

European-Finnish (FIN) AF: 0.0576 AC: 610 AN: 10592

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0853 AC: 5804 AN: 68004

Other (OTH) AF: 0.0482 AC: 102 AN: 2116

Alfa AF: 0.0677 Hom.: 528

Bravo AF: 0.0571

Asia WGS AF: 0.0450 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.10
DANN	Benign	0.47
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2787140; hg19: chr10-8442856;