rs12930697

Positions:

• chr16-61441598-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_933656.1(LOC105371302):​n.98-5261G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

Genes affected

LOC105371302 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105371302	XR_933656.1	n.98-5261G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.605

Alfa AF: 0.591 Hom.: 35062

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12930697; hg19: chr16-61475502;