chr16-8042169-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_197430.1(LOC105371069):​n.335-34945G>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: LOC105371069 NR_197430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315
• Publications: 1 publications found

Genes affected

ENSG00000260289 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_197430.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105371069	NR_197430.1		n.335-34945G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260289	ENST00000567103.2	TSL:5	n.302-34945G>A		intron	N/A
	ENSG00000260289	ENST00000654046.1		n.335-34945G>A		intron	N/A
	ENSG00000260289	ENST00000670665.1		n.335-34945G>A		intron	N/A

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

African (AFR) AF: 0.932 AC: 38729 AN: 41548

American (AMR) AF: 0.944 AC: 14442 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.911 AC: 3162 AN: 3470

East Asian (EAS) AF: 0.902 AC: 4666 AN: 5174

South Asian (SAS) AF: 0.906 AC: 4366 AN: 4818

European-Finnish (FIN) AF: 0.890 AC: 9424 AN: 10590

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.934 AC: 63518 AN: 68030

Other (OTH) AF: 0.940 AC: 1984 AN: 2110

Alfa AF: 0.932 Hom.: 81266

Bravo AF: 0.933

Asia WGS AF: 0.910 AC: 3164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.6
DANN	Benign	0.63
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs6501061; hg19: chr16-8092171;