rs12213875

chr6-14586772-A-G

Variant summary

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

The XR_241980.4(LOC101928354):n.11051T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,964 control chromosomes in the GnomAD database, including 22,588 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 0.51 (22588 hom., cov: 31)
• Consequence: LOC101928354 XR_241980.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

Genes affected

LOC101928354 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928354	XR_241980.4	n.11051T>C		non_coding_transcript_exon_variant	4/4
LOC101928354	XR_001743992.2	n.11189T>C		non_coding_transcript_exon_variant	5/5
LOC101928354	XR_007059472.1	n.11111T>C		non_coding_transcript_exon_variant	4/4
LOC101928354	XR_926516.3	n.11014T>C		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77939 AN: 151848 Hom.: 22599 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.513 AC: 77919 AN: 151964 Hom.: 22588 Cov.: 31 AF XY: 0.513 AC XY: 38121 AN XY: 74254

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.568

Alfa AF: 0.617 Hom.: 22149

Bravo AF: 0.490

Asia WGS AF: 0.540 AC: 1879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	7.1
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12213875; hg19: chr6-14587003;