11-14893332-A-G

Position:

• chr11-14893332-A-G

Variant summary

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

The XR_007062603.1(LOC124902638):​n.1484+4026A>G 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 0.655 in 152,108 control chromosomes in the GnomAD database, including 33,012 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 0.65 (33012 hom., cov: 33)
• Consequence: LOC124902638 XR_007062603.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

Genes affected

LOC124902638 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902638	XR_007062603.1	n.1484+4026A>G		intron_variant, non_coding_transcript_variant
LOC124902638	XR_007062604.1	n.1484+4026A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99456 AN: 151990 Hom.: 32953 Cov.: 33

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.655 AC: 99581 AN: 152108 Hom.: 33012 Cov.: 33 AF XY: 0.658 AC XY: 48924 AN XY: 74358

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.579

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.641

Alfa AF: 0.621 Hom.: 37780

Bravo AF: 0.664

Asia WGS AF: 0.644 AC: 2240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10741657; hg19: chr11-14914878;