rs11048972

chr12-27330924-A-G

Variant summary

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

The XR_007063255.1(LOC124902906):n.176+1698T>C 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 0.0695 in 152,248 control chromosomes in the GnomAD database, including 481 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 0.069 (481 hom., cov: 31)
• Consequence: LOC124902906 XR_007063255.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512

Genes affected

LOC124902906 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902906	XR_007063255.1	n.176+1698T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0695 AC: 10579 AN: 152130 Hom.: 481 Cov.: 31

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.0445

Gnomad ASJ AF: 0.0766

Gnomad EAS AF: 0.0406

Gnomad SAS AF: 0.0497

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0542

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

GnomAD4 genome AF: 0.0695 AC: 10576 AN: 152248 Hom.: 481 Cov.: 31 AF XY: 0.0686 AC XY: 5108 AN XY: 74432

Gnomad4 AFR AF: 0.0165

Gnomad4 AMR AF: 0.0444

Gnomad4 ASJ AF: 0.0766

Gnomad4 EAS AF: 0.0407

Gnomad4 SAS AF: 0.0498

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0541

Alfa AF: 0.0995 Hom.: 111

Bravo AF: 0.0610

Asia WGS AF: 0.0430 AC: 151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.2
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11048972; hg19: chr12-27483857;