rs7632915

chr3-190303659-A-Cchr3-190303659-A-Gchr3-190303659-A-T

Variant summary

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

The NM_001378492.1(CLDN16):c.-445-11234A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 152,056 control chromosomes in the GnomAD database, including 31,453 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 0.64 (31453 hom., cov: 32)
• Consequence: CLDN16 NM_001378492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42

Genes affected

CLDN16 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLDN16	NM_001378492.1	c.-445-11234A>C		intron_variant
CLDN16	NM_001378493.1	c.-279+13068A>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96648 AN: 151938 Hom.: 31407 Cov.: 32

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.636 AC: 96740 AN: 152056 Hom.: 31453 Cov.: 32 AF XY: 0.632 AC XY: 46992 AN XY: 74330

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.749

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.625

Alfa AF: 0.592 Hom.: 42796

Bravo AF: 0.648

Asia WGS AF: 0.547 AC: 1900 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	11
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7632915; hg19: chr3-190021448;