rs16879308

Variant names:

• chr5-51940492-C-T
• rs16879308
• ENST00000771174.1:n.625-2721G>A

Variant summary

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

The ENST00000771174.1(ENSG00000300361):​n.625-2721G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0546 in 152,186 control chromosomes in the GnomAD database, including 232 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 0.055 (232 hom., cov: 33)
• Consequence: ENSG00000300361 ENST00000771174.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 2 publications found

Genes affected

ENSG00000300361 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0703 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000771174.1. 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
	ENSG00000300361	ENST00000771174.1		n.625-2721G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0547 AC: 8312 AN: 152068 Hom.: 232 Cov.: 33

Gnomad AFR AF: 0.0564

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0395

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0757

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0598

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0546 AC: 8316 AN: 152186 Hom.: 232 Cov.: 33 AF XY: 0.0547 AC XY: 4071 AN XY: 74404

African (AFR) AF: 0.0563 AC: 2338 AN: 41522

American (AMR) AF: 0.0395 AC: 603 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0588 AC: 204 AN: 3470

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5172

South Asian (SAS) AF: 0.0768 AC: 370 AN: 4818

European-Finnish (FIN) AF: 0.0569 AC: 603 AN: 10598

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0597 AC: 4062 AN: 68006

Other (OTH) AF: 0.0568 AC: 120 AN: 2112

Alfa AF: 0.0561 Hom.: 108

Bravo AF: 0.0525

Asia WGS AF: 0.0440 AC: 153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.53
PhyloP100		0.28

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: rs16879308;

hg19: chr5-51236326;