rs17804971

chr12-9467109-C-T

Variant summary

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

The NR_153413.2(LOC408186):n.703+5675C>T 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 0.538 in 151,582 control chromosomes in the GnomAD database, including 22,115 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 0.54 (22115 hom., cov: 30)
• Consequence: LOC408186 NR_153413.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730

Genes affected

LOC408186 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC408186	NR_153413.2	n.703+5675C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000641608.1	n.695+5675C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81513 AN: 151468 Hom.: 22102 Cov.: 30

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.538 AC: 81569 AN: 151582 Hom.: 22115 Cov.: 30 AF XY: 0.533 AC XY: 39463 AN XY: 74074

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.519

Alfa AF: 0.554 Hom.: 3991

Bravo AF: 0.537

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.85
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17804971; hg19: chr12-9619705;