rs11807848

Positions:

• chr1-1125786-T-C
• chr1-1125786-T-G

Variant summary

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

The XR_007065349.1(LOC124903819):​n.2141A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,002 control chromosomes in the GnomAD database, including 10,754 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 0.37 (10754 hom., cov: 33)
• Consequence: LOC124903819 XR_007065349.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655

Genes affected

LOC124903819 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903819	XR_007065349.1	n.2141A>G		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56748 AN: 151884 Hom.: 10754 Cov.: 33

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.374 AC: 56774 AN: 152002 Hom.: 10754 Cov.: 33 AF XY: 0.367 AC XY: 27274 AN XY: 74286

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.378

Alfa AF: 0.399 Hom.: 5725

Bravo AF: 0.369

Asia WGS AF: 0.293 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11807848; hg19: chr1-1061166;