rs1397794790

Variant names:

• chr19-41677459-C-A
• NM_001291485.2:c.751G>T

Your query was ambiguous. Multiple possible variants found:

• chr19-41677459-C-A
• chr19-41677459-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001291485.2(CEACAM7):​c.751G>T​(p.Ala251Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,596 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A251T) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: CEACAM7 NM_001291485.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

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 Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.115724444).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEACAM7	NM_001291485.2	c.751G>T	p.Ala251Ser	missense_variant	Exon 4 of 5	ENST00000401731.6	NP_001278414.1
CEACAM7	NM_006890.5	c.751G>T	p.Ala251Ser	missense_variant	Exon 4 of 5		NP_008821.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEACAM7	ENST00000401731.6	c.751G>T	p.Ala251Ser	missense_variant	Exon 4 of 5	2	NM_001291485.2	ENSP00000385932.1
CEACAM7	ENST00000006724.7	c.751G>T	p.Ala251Ser	missense_variant	Exon 4 of 5	1		ENSP00000006724.3
CEACAM7	ENST00000602225.1	c.472G>T	p.Ala158Ser	missense_variant	Exon 3 of 3	1		ENSP00000469597.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461596 Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1 AN XY: 727130

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.67
CADD	Benign	6.2
DANN	Benign	0.93
DEOGEN2	Benign	0.0065	.;.;T
Eigen	Benign	-1.0
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.037	N
LIST_S2	Benign	0.38	.;.;T
M_CAP	Benign	0.0011	T
MetaRNN	Benign	0.12	T;T;T
MetaSVM	Benign	-1.0	T
PrimateAI	Benign	0.28	T
PROVEAN	Benign	0.26	N;N;.
REVEL	Benign	0.046
Sift	Benign	0.093	T;T;.
Sift4G	Benign	0.61	T;T;T
Vest4		0.11
MutPred		0.39		Loss of sheet (P = 0.0181);Loss of sheet (P = 0.0181);.;
MVP		0.085
MPC		0.016
ClinPred		0.15	T
GERP RS		-0.99
gMVP		0.32

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-42181387;