ENST00000420853.1:n.359T>C

Variant names:

• chr1-110491187-T-C
• rs4839431
• ENST00000420853.1:n.359T>C

Variant summary

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

The ENST00000420853.1(CYMP):​n.359T>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 0.872 in 152,662 control chromosomes in the GnomAD database, including 58,210 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 0.87 (58050 hom., cov: 33)
  • Exomes 𝑓: 0.84 (160 hom.)
• Consequence: CYMP ENST00000420853.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.38

Genes affected

CYMP (HGNC:2588): (chymosin, pseudogene)

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 (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYMP	NR_003599.2	n.1159T>C		non_coding_transcript_exon_variant	Exon 9 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYMP	ENST00000420853.1	n.359T>C		non_coding_transcript_exon_variant	Exon 3 of 3	2
CYMP	ENST00000462836.2	n.555T>C		non_coding_transcript_exon_variant	Exon 5 of 5	5
CYMP	ENST00000474680.5	n.1173T>C		non_coding_transcript_exon_variant	Exon 9 of 9	6

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132587 AN: 152086 Hom.: 57996 Cov.: 33

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.870

GnomAD4 exome AF: 0.838 AC: 384 AN: 458 Hom.: 160 Cov.: 0 AF XY: 0.821 AC XY: 230 AN XY: 280

Gnomad4 FIN exome AF: 0.840

Gnomad4 NFE exome AF: 0.909

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.872 AC: 132699 AN: 152204 Hom.: 58050 Cov.: 33 AF XY: 0.868 AC XY: 64561 AN XY: 74390

Gnomad4 AFR AF: 0.928

Gnomad4 AMR AF: 0.880

Gnomad4 ASJ AF: 0.895

Gnomad4 EAS AF: 0.931

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.846

Gnomad4 OTH AF: 0.872

Alfa AF: 0.854 Hom.: 106195

Bravo AF: 0.879

Asia WGS AF: 0.867 AC: 3018 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	0.0040
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4839431; hg19: chr1-111033809;