rs16873479

Variant names:

• chr5-71961573-G-A
• rs16873479
• ENST00000782117.1:n.218-16383G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-71961573-G-A
• chr5-71961573-G-C
• chr5-71961573-G-T

Variant summary

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

The ENST00000782117.1(ENSG00000301834):​n.218-16383G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0468 in 151,636 control chromosomes in the GnomAD database, including 528 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 0.047 (528 hom., cov: 32)
• Consequence: ENSG00000301834 ENST00000782117.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321
• Publications: 2 publications found

Genes affected

ENSG00000301834 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782117.1. 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
	ENSG00000301834	ENST00000782117.1		n.218-16383G>A		intron	N/A
	ENSG00000301834	ENST00000782118.1		n.217-16383G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0467 AC: 7078 AN: 151518 Hom.: 525 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0181

Gnomad ASJ AF: 0.00723

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000416

Gnomad FIN AF: 0.0000961

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00102

Gnomad OTH AF: 0.0393

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

GnomAD4 genome AF: 0.0468 AC: 7098 AN: 151636 Hom.: 528 Cov.: 32 AF XY: 0.0460 AC XY: 3409 AN XY: 74062

African (AFR) AF: 0.160 AC: 6634 AN: 41364

American (AMR) AF: 0.0180 AC: 275 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.00723 AC: 25 AN: 3456

East Asian (EAS) AF: 0.00 AC: 0 AN: 5160

South Asian (SAS) AF: 0.000417 AC: 2 AN: 4800

European-Finnish (FIN) AF: 0.0000961 AC: 1 AN: 10408

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00102 AC: 69 AN: 67882

Other (OTH) AF: 0.0389 AC: 82 AN: 2106

Alfa AF: 0.00955 Hom.: 10

Bravo AF: 0.0536

Asia WGS AF: 0.0110 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.5
DANN	Benign	0.69
PhyloP100		-0.32

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: rs16873479;

hg19: chr5-71257400;