rs11595808

Positions:

• chr10-46193242-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_007062137.1(LOC124902418):​n.9832G>T 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 0.0165 in 151,784 control chromosomes in the GnomAD database, including 45 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 0.016 (45 hom., cov: 32)
• Consequence: LOC124902418 XR_007062137.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

LOC124902418 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0165 (2499/151784) while in subpopulation AMR AF= 0.0284 (433/15238). AF 95% confidence interval is 0.0262. There are 45 homozygotes in gnomad4. There are 1209 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 45 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902418	XR_007062137.1	n.9832G>T		non_coding_transcript_exon_variant	2/2
		n.46193242C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0165 AC: 2499 AN: 151666 Hom.: 44 Cov.: 32

Gnomad AFR AF: 0.00411

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0283

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.0191

Gnomad SAS AF: 0.0181

Gnomad FIN AF: 0.0178

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0200

Gnomad OTH AF: 0.0187

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

GnomAD4 genome AF: 0.0165 AC: 2499 AN: 151784 Hom.: 45 Cov.: 32 AF XY: 0.0163 AC XY: 1209 AN XY: 74236

Gnomad4 AFR AF: 0.00410

Gnomad4 AMR AF: 0.0284

Gnomad4 ASJ AF: 0.0245

Gnomad4 EAS AF: 0.0189

Gnomad4 SAS AF: 0.0181

Gnomad4 FIN AF: 0.0178

Gnomad4 NFE AF: 0.0200

Gnomad4 OTH AF: 0.0185

Alfa AF: 0.0183 Hom.: 3

Bravo AF: 0.0171

Asia WGS AF: 0.0290 AC: 100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.76
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11595808; hg19: chr10-47564478;