8-16579752-T-C

Variant names:

• chr8-16579752-T-C
• rs822318
• XR_007061175.1:n.873-67842A>G

Variant summary

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

The XR_007061175.1(LOC101929028):​n.873-67842A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,712 control chromosomes in the GnomAD database, including 15,706 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 0.45 (15706 hom., cov: 32)
• Consequence: LOC101929028 XR_007061175.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44
• Publications: 3 publications found

Genes affected

LOC101929028 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.651 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: 0.449 AC: 68028 AN: 151594 Hom.: 15697 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.449 AC: 68071 AN: 151712 Hom.: 15706 Cov.: 32 AF XY: 0.448 AC XY: 33222 AN XY: 74158

African (AFR) AF: 0.374 AC: 15492 AN: 41400

American (AMR) AF: 0.393 AC: 5974 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1809 AN: 3462

East Asian (EAS) AF: 0.670 AC: 3451 AN: 5154

South Asian (SAS) AF: 0.545 AC: 2626 AN: 4820

European-Finnish (FIN) AF: 0.441 AC: 4657 AN: 10552

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32401 AN: 67830

Other (OTH) AF: 0.490 AC: 1031 AN: 2104

Alfa AF: 0.478 Hom.: 49305

Bravo AF: 0.444

Asia WGS AF: 0.607 AC: 2105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.40
DANN	Benign	0.25
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs822318; hg19: chr8-16437261;