16-65271607-C-A

Variant names:

• chr16-65271607-C-A
• rs10500517
• ENST00000562656.1:n.271+19738C>A

Variant summary

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

The ENST00000562656.1(ENSG00000260364):​n.271+19738C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0359 in 152,196 control chromosomes in the GnomAD database, including 141 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 0.036 (141 hom., cov: 32)
• Consequence: ENSG00000260364 ENST00000562656.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 1 publications found

Genes affected

ENSG00000260364 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0898 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562656.1. 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
	ENSG00000260364	ENST00000562656.1	TSL:3	n.271+19738C>A		intron	N/A
	ENSG00000260364	ENST00000764865.1		n.194+38427C>A		intron	N/A
	ENSG00000260364	ENST00000764866.1		n.1177+38427C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0358 AC: 5452 AN: 152078 Hom.: 142 Cov.: 32

Gnomad AFR AF: 0.0632

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0206

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.0969

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.00990

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0243

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0359 AC: 5466 AN: 152196 Hom.: 141 Cov.: 32 AF XY: 0.0349 AC XY: 2601 AN XY: 74436

African (AFR) AF: 0.0633 AC: 2627 AN: 41502

American (AMR) AF: 0.0206 AC: 315 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0242 AC: 84 AN: 3468

East Asian (EAS) AF: 0.0968 AC: 501 AN: 5178

South Asian (SAS) AF: 0.0184 AC: 89 AN: 4824

European-Finnish (FIN) AF: 0.00990 AC: 105 AN: 10606

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0243 AC: 1655 AN: 68010

Other (OTH) AF: 0.0289 AC: 61 AN: 2112

Alfa AF: 0.0303 Hom.: 137

Bravo AF: 0.0376

Asia WGS AF: 0.0620 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.74
DANN	Benign	0.50
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10500517;

hg19: chr16-65305510;