10-13422689-C-T

Position:

• chr10-13422689-C-T

Variant summary

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

The ENST00000448272.1(ENSG00000233256):​n.56-46C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.929 in 152,300 control chromosomes in the GnomAD database, including 66,545 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 0.93 (66540 hom., cov: 32)
  • Exomes 𝑓: 1.0 (5 hom.)
• Consequence: ENSG00000233256 ENST00000448272.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

Genes affected

ENSG00000233256 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376420	NR_188196.1	n.570-46C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000233256	ENST00000448272.1	n.56-46C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.929 AC: 141400 AN: 152172 Hom.: 66511 Cov.: 32

Gnomad AFR AF: 0.764

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.992

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.953

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.950

GnomAD4 exome AF: 1.00 AC: 10 AN: 10 Hom.: 5 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.929 AC: 141481 AN: 152290 Hom.: 66540 Cov.: 32 AF XY: 0.931 AC XY: 69335 AN XY: 74464

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.971

Gnomad4 ASJ AF: 0.992

Gnomad4 EAS AF: 0.989

Gnomad4 SAS AF: 0.953

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.998

Gnomad4 OTH AF: 0.948

Alfa AF: 0.984 Hom.: 66661

Bravo AF: 0.922

Asia WGS AF: 0.952 AC: 3311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4748030; hg19: chr10-13464689;