16-61441598-G-A

Variant names:

• chr16-61441598-G-A
• rs12930697
• XR_933656.1:n.98-5261G>A

Variant summary

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

The XR_933656.1(LOC105371302):​n.98-5261G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 151,992 control chromosomes in the GnomAD database, including 26,448 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 0.59 (26448 hom., cov: 33)
• Consequence: LOC105371302 XR_933656.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 5 publications found

Genes affected

LOC105371302 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89141 AN: 151874 Hom.: 26423 Cov.: 33

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.587 AC: 89212 AN: 151992 Hom.: 26448 Cov.: 33 AF XY: 0.579 AC XY: 43022 AN XY: 74322

African (AFR) AF: 0.636 AC: 26360 AN: 41444

American (AMR) AF: 0.540 AC: 8257 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2221 AN: 3468

East Asian (EAS) AF: 0.534 AC: 2751 AN: 5154

South Asian (SAS) AF: 0.477 AC: 2295 AN: 4814

European-Finnish (FIN) AF: 0.476 AC: 5025 AN: 10554

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40374 AN: 67962

Other (OTH) AF: 0.605 AC: 1276 AN: 2110

Alfa AF: 0.590 Hom.: 47500

Bravo AF: 0.595

Asia WGS AF: 0.467 AC: 1623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.60
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs12930697; hg19: chr16-61475502;