XR_948080.3:n.5729A>C

Variant names:

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369526	XR_948080.3	n.5729A>C		non_coding_transcript_exon_variant	Exon 7 of 10
LOC105369526	XR_948081.3	n.5711A>C		non_coding_transcript_exon_variant	Exon 9 of 12
LOC105369526	XR_948082.3	n.5327A>C		non_coding_transcript_exon_variant	Exon 6 of 9
LOC105369526	XR_948083.3	n.5205A>C		non_coding_transcript_exon_variant	Exon 5 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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

Other links and lift over

dbSNP: rs657317; hg19: chr11-119816766;