11-86071625-A-G

Variant names:

• chr11-86071625-A-G
• rs636848
• XR_007062823.1:n.1702A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007062823.1(LOC124902731):​n.1702A>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 0.263 in 152,120 control chromosomes in the GnomAD database, including 5,514 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 0.26 (5514 hom., cov: 32)
• Consequence: LOC124902731 XR_007062823.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346
• Publications: 4 publications found

Genes affected

LOC124902731 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.328 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000845444.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000309910	ENST00000845444.1		n.181-693A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39926 AN: 152004 Hom.: 5515 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.263 AC: 39946 AN: 152120 Hom.: 5514 Cov.: 32 AF XY: 0.259 AC XY: 19275 AN XY: 74362

African (AFR) AF: 0.333 AC: 13811 AN: 41496

American (AMR) AF: 0.272 AC: 4158 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 865 AN: 3464

East Asian (EAS) AF: 0.131 AC: 679 AN: 5184

South Asian (SAS) AF: 0.282 AC: 1361 AN: 4820

European-Finnish (FIN) AF: 0.149 AC: 1581 AN: 10594

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16530 AN: 67956

Other (OTH) AF: 0.258 AC: 544 AN: 2110

Alfa AF: 0.225 Hom.: 1494

Bravo AF: 0.273

Asia WGS AF: 0.186 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.77
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs636848; hg19: chr11-85782667;