Variant 19-44719328-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_186814.1(CEACAM16-AS1):n.349-3245A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,888 control chromosomes in the GnomAD database, including 25,131 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 0.57 ( 25131 hom., cov: 30)

Consequence

CEACAM16-AS1
NR_186814.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.172

Variant links:

Genes affected

CEACAM16-AS1 (HGNC:55317): (CEACAM16, CEACAM19 and PVR antisense RNA 1)

CEACAM16-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEACAM16-AS1	NR_186814.1 link	n.349-3245A>C		intron_variant
CEACAM16-AS1	NR_186815.1 link	n.347+5509A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect
CEACAM16-AS1	ENST00000657348.1 link	n.352-3245A>C	intron_variant
CEACAM16-AS1	ENST00000662585.1 link	n.381+5509A>C	intron_variant
CEACAM16-AS1	ENST00000702856.1 link	n.347+5509A>C	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.572

AC:

86885

AN:

151770

Hom.:

25095

Cov.:

show subpopulations

Gnomad AFR

AF:

0.632

Gnomad AMI

AF:

0.435

Gnomad AMR

AF:

0.468

Gnomad ASJ

AF:

0.426

Gnomad EAS

AF:

0.587

Gnomad SAS

AF:

0.669

Gnomad FIN

AF:

0.533

Gnomad MID

AF:

0.561

Gnomad NFE

AF:

0.569

Gnomad OTH

AF:

0.532

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

GnomAD4 genome

AF:

0.573

AC:

86957

AN:

151888

Hom.:

25131

Cov.:

AF XY:

0.570

AC XY:

42299

AN XY:

74254

show subpopulations

Gnomad4 AFR

AF:

0.632

Gnomad4 AMR

AF:

0.467

Gnomad4 ASJ

AF:

0.426

Gnomad4 EAS

AF:

0.587

Gnomad4 SAS

AF:

0.670

Gnomad4 FIN

AF:

0.533

Gnomad4 NFE

AF:

0.569

Gnomad4 OTH

AF:

0.535

Alfa

AF:

0.555

Hom.:

30575

Bravo

AF:

0.564

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

7.1

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over