rs10501192

chr11-38245666-C-T

Variant summary

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

The XR_931202.2(LOC105376634):n.555-44618G>A 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 0.0799 in 151,594 control chromosomes in the GnomAD database, including 1,567 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 0.080 (1567 hom., cov: 32)
• Consequence: LOC105376634 XR_931202.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.925

Genes affected

LOC105376634 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376634	XR_931202.2	n.555-44618G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0797 AC: 12070 AN: 151476 Hom.: 1557 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0284

Gnomad ASJ AF: 0.00896

Gnomad EAS AF: 0.0236

Gnomad SAS AF: 0.00786

Gnomad FIN AF: 0.00472

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00547

Gnomad OTH AF: 0.0615

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

GnomAD4 genome AF: 0.0799 AC: 12115 AN: 151594 Hom.: 1567 Cov.: 32 AF XY: 0.0773 AC XY: 5728 AN XY: 74104

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.0283

Gnomad4 ASJ AF: 0.00896

Gnomad4 EAS AF: 0.0234

Gnomad4 SAS AF: 0.00829

Gnomad4 FIN AF: 0.00472

Gnomad4 NFE AF: 0.00547

Gnomad4 OTH AF: 0.0613

Alfa AF: 0.0501 Hom.: 102

Bravo AF: 0.0898

Asia WGS AF: 0.0330 AC: 116 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.32
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501192; hg19: chr11-38267216;