11-102268172-G-A

Position:

• chr11-102268172-G-A

Variant summary

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

The XR_007062863.1(LOC105369460):​n.126-958G>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 0.236 in 151,912 control chromosomes in the GnomAD database, including 4,445 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 0.24 (4445 hom., cov: 32)
• Consequence: LOC105369460 XR_007062863.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.747

Genes affected

LOC105369460 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369460	XR_007062863.1	n.126-958G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35834 AN: 151796 Hom.: 4438 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.236 AC: 35861 AN: 151912 Hom.: 4445 Cov.: 32 AF XY: 0.238 AC XY: 17658 AN XY: 74254

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.220

Alfa AF: 0.225 Hom.: 2224

Bravo AF: 0.233

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2124216; hg19: chr11-102138903;