rs10520341

chr19-41676643-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001291485.2(CEACAM7):c.*36+733C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,144 control chromosomes in the GnomAD database, including 5,026 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 0.24 (5026 hom., cov: 32)
• Consequence: CEACAM7 NM_001291485.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEACAM7	NM_001291485.2	c.*36+733C>T		intron_variant		ENST00000401731.6
CEACAM7	NM_006890.5	c.*36+733C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEACAM7	ENST00000401731.6	c.*36+733C>T		intron_variant		2	NM_001291485.2	P1
CEACAM7	ENST00000006724.7	c.*36+733C>T		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36735 AN: 152024 Hom.: 5027 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.241 AC: 36736 AN: 152144 Hom.: 5026 Cov.: 32 AF XY: 0.246 AC XY: 18327 AN XY: 74364

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.265

Alfa AF: 0.254 Hom.: 667

Bravo AF: 0.236

Asia WGS AF: 0.330 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.68
Dann	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520341; hg19: chr19-42180571;