rs17724225

Variant names:

• chr19-41558140-T-C
• rs17724225
• NM_001288773.3:c.-778-6542T>C

Variant summary

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

The NM_001288773.3(CEACAM21):​c.-778-6542T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0492 in 152,278 control chromosomes in the GnomAD database, including 494 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 0.049 (494 hom., cov: 32)
• Consequence: CEACAM21 NM_001288773.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 0 publications found

Genes affected

CEACAM21 (HGNC:28834): (CEA cell adhesion molecule 21) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEACAM21	NM_001288773.3	c.-778-6542T>C		intron_variant	Intron 1 of 7		NP_001275702.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEACAM21	ENST00000407170.6	c.-778-6542T>C		intron_variant	Intron 1 of 7	2		ENSP00000384380.1
CEACAM21	ENST00000618577.4	n.36-6542T>C		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.0493 AC: 7498 AN: 152160 Hom.: 495 Cov.: 32

Gnomad AFR AF: 0.0454

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0347

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0646

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0230

Gnomad OTH AF: 0.0503

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

GnomAD4 genome AF: 0.0492 AC: 7489 AN: 152278 Hom.: 494 Cov.: 32 AF XY: 0.0545 AC XY: 4060 AN XY: 74458

African (AFR) AF: 0.0453 AC: 1881 AN: 41568

American (AMR) AF: 0.0346 AC: 530 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0464 AC: 161 AN: 3472

East Asian (EAS) AF: 0.363 AC: 1881 AN: 5180

South Asian (SAS) AF: 0.123 AC: 593 AN: 4818

European-Finnish (FIN) AF: 0.0646 AC: 686 AN: 10616

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0230 AC: 1566 AN: 68008

Other (OTH) AF: 0.0531 AC: 112 AN: 2110

Alfa AF: 0.0356 Hom.: 22

Bravo AF: 0.0471

Asia WGS AF: 0.241 AC: 837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.2
DANN	Benign	0.34
PhyloP100		-0.64
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs17724225; hg19: chr19-42064510;