rs11239762

Positions:

• chr10-42766813-G-A

Variant summary

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

The NR_134498.1(LOC105378269):​n.285-2466G>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 0.11 in 152,078 control chromosomes in the GnomAD database, including 1,091 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 0.11 (1091 hom., cov: 32)
• Consequence: LOC105378269 NR_134498.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

LOC105378269 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378269	NR_134498.1	n.285-2466G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16735 AN: 151960 Hom.: 1080 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0253

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0743

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.110 AC: 16770 AN: 152078 Hom.: 1091 Cov.: 32 AF XY: 0.112 AC XY: 8333 AN XY: 74326

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.0247

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0743

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0894 Hom.: 361

Bravo AF: 0.113

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	-0.83
CADD	Benign	0.99
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11239762; hg19: chr10-43262261;