rs11807848

Variant names:

• chr1-1125786-T-C
• rs11807848
• XR_007065349.1:n.2141A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-1125786-T-C
• chr1-1125786-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

LOC124903819 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.353 AC: 14656 AN: 41462

American (AMR) AF: 0.316 AC: 4829 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1351 AN: 3472

East Asian (EAS) AF: 0.229 AC: 1181 AN: 5158

South Asian (SAS) AF: 0.364 AC: 1752 AN: 4818

European-Finnish (FIN) AF: 0.369 AC: 3896 AN: 10562

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27770 AN: 67940

Other (OTH) AF: 0.378 AC: 798 AN: 2110

Alfa AF: 0.400 Hom.: 6370

Bravo AF: 0.369

Asia WGS AF: 0.293 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.37
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs11807848; hg19: chr1-1061166;