rs16941835

Variant names:

• chr16-86662114-G-C
• rs16941835
• ENST00000565822.1:n.328-6629G>C

Variant summary

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

The ENST00000565822.1(ENSG00000261161):​n.328-6629G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,042 control chromosomes in the GnomAD database, including 3,264 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 0.20 (3264 hom., cov: 33)
• Consequence: ENSG00000261161 ENST00000565822.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.854
• Publications: 15 publications found

Genes affected

ENSG00000261161 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565822.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261161	ENST00000565822.1	TSL:3	n.328-6629G>C		intron	N/A
	ENSG00000261161	ENST00000808928.1		n.854+14758G>C		intron	N/A
	ENSG00000261161	ENST00000808929.1		n.721+14915G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31072 AN: 151924 Hom.: 3264 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.205 AC: 31099 AN: 152042 Hom.: 3264 Cov.: 33 AF XY: 0.205 AC XY: 15248 AN XY: 74314

African (AFR) AF: 0.198 AC: 8207 AN: 41478

American (AMR) AF: 0.201 AC: 3071 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 398 AN: 3468

East Asian (EAS) AF: 0.314 AC: 1623 AN: 5174

South Asian (SAS) AF: 0.173 AC: 834 AN: 4822

European-Finnish (FIN) AF: 0.222 AC: 2346 AN: 10548

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13948 AN: 67964

Other (OTH) AF: 0.199 AC: 419 AN: 2110

Alfa AF: 0.211 Hom.: 410

Bravo AF: 0.203

Asia WGS AF: 0.212 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.8
DANN	Benign	0.61
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs16941835; hg19: chr16-86695720;