rs9284326

Positions:

• chr16-18071186-A-C
• chr16-18071186-A-G
• chr16-18071186-A-T

Variant summary

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

The ENST00000563866.1(ENSG00000260242):​n.49-67738T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,076 control chromosomes in the GnomAD database, including 14,322 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 0.43 (14322 hom., cov: 32)
• Consequence: ENST00000563866.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000563866.1	n.49-67738T>G		intron_variant, non_coding_transcript_variant		3
	ENST00000567304.1	n.144+80266T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65538 AN: 151956 Hom.: 14312 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.431 AC: 65597 AN: 152076 Hom.: 14322 Cov.: 32 AF XY: 0.433 AC XY: 32194 AN XY: 74346

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.455

Alfa AF: 0.434 Hom.: 17246

Bravo AF: 0.427

Asia WGS AF: 0.479 AC: 1666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.011
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9284326; hg19: chr16-18165043;