rs615932

Variant names:

• chr11-102855974-G-A
• rs615932
• XR_007062868.1:n.1991+191G>A

Variant summary

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

The XR_007062868.1(LOC124902741):​n.1991+191G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0968 in 152,124 control chromosomes in the GnomAD database, including 979 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 0.097 (979 hom., cov: 32)
• Consequence: LOC124902741 XR_007062868.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216
• Publications: 5 publications found

Genes affected

LOC124902741 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 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: 0.0969 AC: 14723 AN: 152006 Hom.: 975 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0995

Gnomad FIN AF: 0.0409

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0527

Gnomad OTH AF: 0.0971

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

GnomAD4 genome AF: 0.0968 AC: 14729 AN: 152124 Hom.: 979 Cov.: 32 AF XY: 0.0953 AC XY: 7089 AN XY: 74354

African (AFR) AF: 0.188 AC: 7800 AN: 41468

American (AMR) AF: 0.0693 AC: 1060 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3468

East Asian (EAS) AF: 0.110 AC: 570 AN: 5178

South Asian (SAS) AF: 0.0983 AC: 473 AN: 4812

European-Finnish (FIN) AF: 0.0409 AC: 433 AN: 10580

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0527 AC: 3587 AN: 68012

Other (OTH) AF: 0.101 AC: 214 AN: 2112

Alfa AF: 0.0818 Hom.: 119

Bravo AF: 0.103

Asia WGS AF: 0.112 AC: 391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.79
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs615932; hg19: chr11-102726705; COSMIC: COSV70064524;