16-8042169-C-T

Variant names:

• chr16-8042169-C-T
• rs6501061
• ENST00000567103.2:n.302-34945G>A

Variant summary

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

The ENST00000567103.2(ENSG00000260289):​n.302-34945G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.929 in 152,252 control chromosomes in the GnomAD database, including 65,697 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 0.93 (65697 hom., cov: 32)
• Consequence: ENSG00000260289 ENST00000567103.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315

Genes affected

ENSG00000260289 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260289	ENST00000567103.2	n.302-34945G>A		intron_variant	Intron 1 of 3	5
ENSG00000260289	ENST00000654046.1	n.335-34945G>A		intron_variant	Intron 1 of 3
ENSG00000260289	ENST00000670665.1	n.335-34945G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.929 AC: 141324 AN: 152134 Hom.: 65636 Cov.: 32

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.934

Gnomad OTH AF: 0.940

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

GnomAD4 genome AF: 0.929 AC: 141444 AN: 152252 Hom.: 65697 Cov.: 32 AF XY: 0.926 AC XY: 68955 AN XY: 74432

Gnomad4 AFR AF: 0.932

Gnomad4 AMR AF: 0.944

Gnomad4 ASJ AF: 0.911

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.906

Gnomad4 FIN AF: 0.890

Gnomad4 NFE AF: 0.934

Gnomad4 OTH AF: 0.940

Alfa AF: 0.931 Hom.: 61468

Bravo AF: 0.933

Asia WGS AF: 0.910 AC: 3164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6501061; hg19: chr16-8092171;