19-43303030-G-T

Variant names:

• chr19-43303030-G-T
• rs5009916
• ENST00000457676.1:n.*141C>A

Variant summary

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

The ENST00000457676.1(CEACAMP4):​n.*141C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 382,764 control chromosomes in the GnomAD database, including 19,714 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 0.33 (8479 hom., cov: 31)
  • Exomes 𝑓: 0.30 (11235 hom.)
• Consequence: CEACAMP4 ENST00000457676.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190
• Publications: 4 publications found

Genes affected

CEACAMP4 (HGNC:1826): (CEA cell adhesion molecule pseudogene 4)

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 = 0.342 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000457676.1. 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
	CEACAMP4	ENST00000457676.1	TSL:6	n.*141C>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50083 AN: 151676 Hom.: 8474 Cov.: 31

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.315

GnomAD4 exome AF: 0.302 AC: 69727 AN: 230970 Hom.: 11235 AF XY: 0.297 AC XY: 40383 AN XY: 136120

African (AFR) AF: 0.320 AC: 1449 AN: 4522

American (AMR) AF: 0.240 AC: 4065 AN: 16932

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 1393 AN: 4960

East Asian (EAS) AF: 0.351 AC: 2488 AN: 7088

South Asian (SAS) AF: 0.212 AC: 8816 AN: 41528

European-Finnish (FIN) AF: 0.315 AC: 4933 AN: 15676

Middle Eastern (MID) AF: 0.214 AC: 154 AN: 718

European-Non Finnish (NFE) AF: 0.334 AC: 43127 AN: 128972

Other (OTH) AF: 0.312 AC: 3302 AN: 10574

GnomAD4 genome AF: 0.330 AC: 50119 AN: 151794 Hom.: 8479 Cov.: 31 AF XY: 0.324 AC XY: 24031 AN XY: 74182

African (AFR) AF: 0.341 AC: 14112 AN: 41374

American (AMR) AF: 0.292 AC: 4447 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1072 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1827 AN: 5150

South Asian (SAS) AF: 0.215 AC: 1036 AN: 4812

European-Finnish (FIN) AF: 0.300 AC: 3160 AN: 10534

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23463 AN: 67896

Other (OTH) AF: 0.315 AC: 664 AN: 2106

Alfa AF: 0.333 Hom.: 25367

Bravo AF: 0.331

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.66
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs5009916; hg19: chr19-43807182;