rs5009916

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr19-43303030-G-C
• chr19-43303030-G-T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000457676.1(CEACAMP4):​n.*141C>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00267 in 383,960 control chromosomes in the GnomAD database, including 9 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 0.0029 (6 hom., cov: 31)
  • Exomes 𝑓: 0.0025 (3 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS2: High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEACAMP4	ENST00000457676.1	n.*141C>G		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.00293 AC: 444 AN: 151774 Hom.: 6 Cov.: 31

Gnomad AFR AF: 0.000315

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00112

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00265

Gnomad OTH AF: 0.00239

GnomAD4 exome AF: 0.00251 AC: 583 AN: 232068 Hom.: 3 AF XY: 0.00248 AC XY: 339 AN XY: 136734

African (AFR) AF: 0.000220 AC: 1 AN: 4544

American (AMR) AF: 0.00123 AC: 21 AN: 17010

Ashkenazi Jewish (ASJ) AF: 0.0122 AC: 61 AN: 4992

East Asian (EAS) AF: 0.00 AC: 0 AN: 7122

South Asian (SAS) AF: 0.000552 AC: 23 AN: 41702

European-Finnish (FIN) AF: 0.0123 AC: 193 AN: 15740

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 720

European-Non Finnish (NFE) AF: 0.00194 AC: 251 AN: 129618

Other (OTH) AF: 0.00311 AC: 33 AN: 10620

GnomAD4 genome AF: 0.00292 AC: 444 AN: 151892 Hom.: 6 Cov.: 31 AF XY: 0.00345 AC XY: 256 AN XY: 74240

African (AFR) AF: 0.000314 AC: 13 AN: 41420

American (AMR) AF: 0.00111 AC: 17 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0159 AC: 55 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5152

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4814

European-Finnish (FIN) AF: 0.0164 AC: 173 AN: 10542

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00265 AC: 180 AN: 67920

Other (OTH) AF: 0.00237 AC: 5 AN: 2110

Alfa AF: 0.0000228 Hom.: 25367

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.60
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;