chr19-41684843-T-C

Variant names:

• chr19-41684843-T-C
• rs7251886
• NM_001291485.2:c.428-780A>G

Variant summary

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

The NM_001291485.2(CEACAM7):​c.428-780A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 152,064 control chromosomes in the GnomAD database, including 20,284 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 0.51 (20284 hom., cov: 33)
• Consequence: CEACAM7 NM_001291485.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.05
• Publications: 5 publications found

Genes affected

CEACAM7 (HGNC:1819): (CEA cell adhesion molecule 7) This gene encodes a cell surface glycoprotein and member of the carcinoembryonic antigen (CEA) family of proteins. Expression of this gene may be downregulated in colon and rectal cancer. Additionally, lower expression levels of this gene may be predictive of rectal cancer recurrence. This gene is present in a CEA family gene cluster on chromosome 19. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]

ENSG00000308584 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001291485.2. 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
	CEACAM7	NM_001291485.2	MANE Select	c.428-780A>G		intron	N/A	NP_001278414.1	Q14002-1
	CEACAM7	NM_006890.5		c.428-780A>G		intron	N/A	NP_008821.2	Q14002-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAM7	ENST00000401731.6	TSL:2 MANE Select	c.428-780A>G		intron	N/A	ENSP00000385932.1	Q14002-1
	CEACAM7	ENST00000006724.7	TSL:1	c.428-780A>G		intron	N/A	ENSP00000006724.3	Q14002-1
	CEACAM7	ENST00000602225.1	TSL:1	c.427+2016A>G		intron	N/A	ENSP00000469597.1	Q14002-2

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78095 AN: 151946 Hom.: 20278 Cov.: 33

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.551

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.514 AC: 78130 AN: 152064 Hom.: 20284 Cov.: 33 AF XY: 0.514 AC XY: 38239 AN XY: 74324

African (AFR) AF: 0.413 AC: 17130 AN: 41450

American (AMR) AF: 0.578 AC: 8841 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1978 AN: 3472

East Asian (EAS) AF: 0.505 AC: 2614 AN: 5176

South Asian (SAS) AF: 0.504 AC: 2429 AN: 4824

European-Finnish (FIN) AF: 0.510 AC: 5388 AN: 10568

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37746 AN: 67970

Other (OTH) AF: 0.548 AC: 1156 AN: 2110

Alfa AF: 0.544 Hom.: 9767

Bravo AF: 0.521

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
PhyloP100		-4.1

Splicing

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

Other links and lift over

dbSNP: rs7251886; hg19: chr19-42188775;