rs12930697

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371302	XR_933656.1	n.98-5261G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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 v4.3

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;