rs11199874

Positions:

• chr10-121273005-G-A

Variant summary

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

The XR_007062321.1(LOC105378523):​n.515+40211C>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 0.228 in 152,084 control chromosomes in the GnomAD database, including 4,206 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 0.23 (4206 hom., cov: 32)
• Consequence: LOC105378523 XR_007062321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

Genes affected

LOC105378523 (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 (AMR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378523	XR_007062321.1	n.515+40211C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34723 AN: 151966 Hom.: 4204 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.228 AC: 34730 AN: 152084 Hom.: 4206 Cov.: 32 AF XY: 0.229 AC XY: 17054 AN XY: 74346

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.253

Alfa AF: 0.250 Hom.: 4329

Bravo AF: 0.225

Asia WGS AF: 0.193 AC: 670 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	0.098
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11199874; hg19: chr10-123032519;