rs11598854

Positions:

• chr10-20608974-C-T

Variant summary

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

The XR_007062080.1(LOC105376442):​n.429-887C>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 0.105 in 152,144 control chromosomes in the GnomAD database, including 1,175 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 0.10 (1175 hom., cov: 31)
• Consequence: LOC105376442 XR_007062080.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.789

Genes affected

LOC105376442 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376442	XR_007062080.1	n.429-887C>T		intron_variant, non_coding_transcript_variant
LOC105376442	XR_007062081.1	n.533-887C>T		intron_variant, non_coding_transcript_variant
LOC105376442	XR_930729.3	n.578-887C>T		intron_variant, non_coding_transcript_variant
LOC105376442	XR_930733.3	n.624-887C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15914 AN: 152026 Hom.: 1174 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0803

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.0865

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0278

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0634

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.105 AC: 15924 AN: 152144 Hom.: 1175 Cov.: 31 AF XY: 0.102 AC XY: 7605 AN XY: 74374

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.0801

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.0866

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0278

Gnomad4 NFE AF: 0.0634

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0811 Hom.: 1081

Bravo AF: 0.115

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11598854; hg19: chr10-20897903;