rs657317

Variant names:

• chr11-119946057-A-C
• rs657317
• XR_948080.3:n.5729A>C

Your query was ambiguous. Multiple possible variants found:

• chr11-119946057-A-C
• chr11-119946057-A-G
• chr11-119946057-A-T

Variant summary

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

The XR_948080.3(LOC105369526):​n.5729A>C 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 0.927 in 152,202 control chromosomes in the GnomAD database, including 65,707 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 0.93 (65707 hom., cov: 31)
• Consequence: LOC105369526 XR_948080.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 4 publications found

Genes affected

LOC105369526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.927 AC: 141029 AN: 152084 Hom.: 65675 Cov.: 31

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.970

Gnomad OTH AF: 0.942

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

GnomAD4 genome AF: 0.927 AC: 141115 AN: 152202 Hom.: 65707 Cov.: 31 AF XY: 0.927 AC XY: 68954 AN XY: 74402

African (AFR) AF: 0.828 AC: 34360 AN: 41514

American (AMR) AF: 0.955 AC: 14610 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.976 AC: 3387 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5152 AN: 5156

South Asian (SAS) AF: 0.970 AC: 4668 AN: 4812

European-Finnish (FIN) AF: 0.933 AC: 9896 AN: 10606

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.970 AC: 65986 AN: 68024

Other (OTH) AF: 0.943 AC: 1993 AN: 2114

Alfa AF: 0.948 Hom.: 5591

Bravo AF: 0.926

Asia WGS AF: 0.972 AC: 3381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.8
DANN	Benign	0.82
PhyloP100		-0.32

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs657317;

hg19: chr11-119816766;