rs12220927

Positions:

• chr10-88230790-T-G

Variant summary

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

The XR_001747537.3(LOC101929727):​n.442+98237T>G 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 0.133 in 152,308 control chromosomes in the GnomAD database, including 1,527 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 0.13 (1527 hom., cov: 34)
• Consequence: LOC101929727 XR_001747537.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

Genes affected

LOC101929727 (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 (SAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929727	XR_001747537.3	n.442+98237T>G		intron_variant, non_coding_transcript_variant
RNLS	XM_011539924.4	c.*28+44143A>C		intron_variant			XP_011538226.1
RNLS	XM_017016382.3	c.*28+44143A>C		intron_variant			XP_016871871.1
RNLS	XR_001747122.3	n.1104+44143A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20308 AN: 152190 Hom.: 1530 Cov.: 34

Gnomad AFR AF: 0.0868

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.00846

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.133 AC: 20309 AN: 152308 Hom.: 1527 Cov.: 34 AF XY: 0.130 AC XY: 9693 AN XY: 74474

Gnomad4 AFR AF: 0.0866

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.00847

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.160

Alfa AF: 0.161 Hom.: 2757

Bravo AF: 0.126

Asia WGS AF: 0.0970 AC: 337 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	3.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12220927; hg19: chr10-89990547;