chr3-190297911-T-G

Position:

• chr3-190297911-T-G

Variant summary

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

The NM_001378492.1(CLDN16):​c.-446+7320T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 151,280 control chromosomes in the GnomAD database, including 43,133 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 0.75 (43133 hom., cov: 29)
• Consequence: CLDN16 NM_001378492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371

Genes affected

CLDN16 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLDN16	NM_001378492.1	c.-446+7320T>G		intron_variant
CLDN16	NM_001378493.1	c.-279+7320T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.750 AC: 113331 AN: 151166 Hom.: 43083 Cov.: 29

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.750 AC: 113438 AN: 151280 Hom.: 43133 Cov.: 29 AF XY: 0.749 AC XY: 55307 AN XY: 73820

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.741

Alfa AF: 0.703 Hom.: 34133

Bravo AF: 0.761

Asia WGS AF: 0.643 AC: 2235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6776530; hg19: chr3-190015700;