chr1-110491187-T-C

Variant names:

• chr1-110491187-T-C
• rs4839431
• ENST00000420853.2:n.1064T>C

Variant summary

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

The ENST00000420853.2(ENSG00000283999):​n.1064T>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: ENSG00000283999 ENST00000420853.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.38
• Publications: 10 publications found

Genes affected

ENSG00000283999 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420853.2. 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
	CYMP	NR_003599.2		n.1159T>C		non_coding_transcript_exon	Exon 9 of 9

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283999	ENST00000420853.2	TSL:2	n.1064T>C		non_coding_transcript_exon	Exon 8 of 8
	ENSG00000283999	ENST00000462836.2	TSL:5	n.555T>C		non_coding_transcript_exon	Exon 5 of 5
	CYMP	ENST00000474680.5	TSL:6	n.1173T>C		non_coding_transcript_exon	Exon 9 of 9

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

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) AF: 0.840 AC: 361 AN: 430

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.909 AC: 20 AN: 22

Other (OTH) AF: 0.500 AC: 3 AN: 6

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

African (AFR) AF: 0.928 AC: 38539 AN: 41524

American (AMR) AF: 0.880 AC: 13470 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3108 AN: 3472

East Asian (EAS) AF: 0.931 AC: 4825 AN: 5184

South Asian (SAS) AF: 0.802 AC: 3864 AN: 4816

European-Finnish (FIN) AF: 0.811 AC: 8574 AN: 10574

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.846 AC: 57532 AN: 68014

Other (OTH) AF: 0.872 AC: 1843 AN: 2114

Alfa AF: 0.856 Hom.: 228136

Bravo AF: 0.879

Asia WGS AF: 0.867 AC: 3018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0040
DANN	Benign	0.31
PhyloP100		-5.4

Splicing

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

Other links and lift over

dbSNP: rs4839431; hg19: chr1-111033809;