16-30811726-G-T

Variant names:

• chr16-30811726-G-T
• rs4889490
• XR_007065052.1:n.112-9131G>T

Variant summary

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

The XR_007065052.1(LOC124903679):​n.112-9131G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 150,434 control chromosomes in the GnomAD database, including 10,954 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 0.33 (10954 hom., cov: 28)
• Consequence: LOC124903679 XR_007065052.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633
• Publications: 26 publications found

Genes affected

LOC124903679 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.330 AC: 49619 AN: 150316 Hom.: 10941 Cov.: 28

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.330 AC: 49640 AN: 150434 Hom.: 10954 Cov.: 28 AF XY: 0.333 AC XY: 24358 AN XY: 73222

African (AFR) AF: 0.0770 AC: 3165 AN: 41086

American (AMR) AF: 0.498 AC: 7322 AN: 14716

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1545 AN: 3456

East Asian (EAS) AF: 0.889 AC: 4572 AN: 5140

South Asian (SAS) AF: 0.195 AC: 926 AN: 4754

European-Finnish (FIN) AF: 0.410 AC: 4221 AN: 10286

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26609 AN: 67720

Other (OTH) AF: 0.387 AC: 805 AN: 2080

Alfa AF: 0.389 Hom.: 20244

Bravo AF: 0.338

Asia WGS AF: 0.471 AC: 1641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.20
DANN	Benign	0.45
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs4889490; hg19: chr16-30823047;