chr19-41684843-T-C

Position:

• chr19-41684843-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEACAM7	NM_001291485.2	c.428-780A>G		intron_variant		ENST00000401731.6	NP_001278414.1
CEACAM7	NM_006890.5	c.428-780A>G		intron_variant			NP_008821.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEACAM7	ENST00000401731.6	c.428-780A>G		intron_variant		2	NM_001291485.2	ENSP00000385932	P1
CEACAM7	ENST00000006724.7	c.428-780A>G		intron_variant		1		ENSP00000006724	P1
CEACAM7	ENST00000602225.1	c.427+2016A>G		intron_variant		1		ENSP00000469597
CEACAM7	ENST00000599715.1	n.524-780A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.548

Alfa AF: 0.546 Hom.: 8023

Bravo AF: 0.521

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7251886; hg19: chr19-42188775;