rs4803481

chr19-41560186-G-A

Variant summary

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

The NM_001288773.3(CEACAM21):c.-778-4496G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 152,032 control chromosomes in the GnomAD database, including 17,030 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 0.42 (17030 hom., cov: 32)
• Consequence: CEACAM21 NM_001288773.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEACAM21	NM_001288773.3	c.-778-4496G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEACAM21	ENST00000407170.6	c.-778-4496G>A		intron_variant		2
CEACAM21	ENST00000618577.4	n.36-4496G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63312 AN: 151912 Hom.: 16980 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.417 AC: 63410 AN: 152032 Hom.: 17030 Cov.: 32 AF XY: 0.416 AC XY: 30950 AN XY: 74314

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.376

Alfa AF: 0.295 Hom.: 4336

Bravo AF: 0.426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4803481; hg19: chr19-42066556;