XR_933752.3:n.243+709A>G

Variant names:

• chr16-77468289-T-C
• rs1826601
• XR_933752.3:n.243+709A>G

Variant summary

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

The XR_933752.3(LOC105376775):​n.243+709A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,944 control chromosomes in the GnomAD database, including 17,030 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 0.46 (17030 hom., cov: 31)
• Consequence: LOC105376775 XR_933752.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 5 publications found

Genes affected

LOC105376775 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69965 AN: 151826 Hom.: 17013 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.461 AC: 70021 AN: 151944 Hom.: 17030 Cov.: 31 AF XY: 0.454 AC XY: 33706 AN XY: 74242

African (AFR) AF: 0.326 AC: 13502 AN: 41436

American (AMR) AF: 0.396 AC: 6037 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1768 AN: 3470

East Asian (EAS) AF: 0.232 AC: 1196 AN: 5160

South Asian (SAS) AF: 0.419 AC: 2017 AN: 4816

European-Finnish (FIN) AF: 0.492 AC: 5192 AN: 10554

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38555 AN: 67938

Other (OTH) AF: 0.471 AC: 992 AN: 2106

Alfa AF: 0.519 Hom.: 11885

Bravo AF: 0.448

Asia WGS AF: 0.345 AC: 1198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.48
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1826601; hg19: chr16-77502186;