rs654600

Variant names:

• chr11-102858443-A-C
• rs654600
• XR_007062868.1:n.1991+2660A>C

Your query was ambiguous. Multiple possible variants found:

• chr11-102858443-A-C
• chr11-102858443-A-G

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+2660A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 151,944 control chromosomes in the GnomAD database, including 3,676 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 0.21 (3676 hom., cov: 31)
• Consequence: LOC124902741 XR_007062868.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.951
• Publications: 10 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 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: 0.213 AC: 32324 AN: 151826 Hom.: 3673 Cov.: 31

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.213 AC: 32336 AN: 151944 Hom.: 3676 Cov.: 31 AF XY: 0.212 AC XY: 15739 AN XY: 74286

African (AFR) AF: 0.290 AC: 12017 AN: 41410

American (AMR) AF: 0.148 AC: 2252 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 827 AN: 3470

East Asian (EAS) AF: 0.136 AC: 705 AN: 5184

South Asian (SAS) AF: 0.172 AC: 827 AN: 4812

European-Finnish (FIN) AF: 0.246 AC: 2602 AN: 10556

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12374 AN: 67930

Other (OTH) AF: 0.209 AC: 442 AN: 2114

Alfa AF: 0.0994 Hom.: 150

Bravo AF: 0.209

Asia WGS AF: 0.170 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.55
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs654600; hg19: chr11-102729174;