chr8-72526835-A-G

Variant names:

• chr8-72526835-A-G
• rs1431659
• XR_929042.3:n.797+4715T>C

Variant summary

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

The XR_929042.3(LOC105375897):​n.797+4715T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 151,994 control chromosomes in the GnomAD database, including 41,518 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 0.74 (41518 hom., cov: 31)
• Consequence: LOC105375897 XR_929042.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.951
• Publications: 10 publications found

Genes affected

LOC105375897 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.78 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: 0.738 AC: 112127 AN: 151876 Hom.: 41476 Cov.: 31

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.738 AC: 112222 AN: 151994 Hom.: 41518 Cov.: 31 AF XY: 0.740 AC XY: 54917 AN XY: 74262

African (AFR) AF: 0.741 AC: 30698 AN: 41444

American (AMR) AF: 0.792 AC: 12088 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2539 AN: 3466

East Asian (EAS) AF: 0.696 AC: 3588 AN: 5154

South Asian (SAS) AF: 0.645 AC: 3102 AN: 4808

European-Finnish (FIN) AF: 0.764 AC: 8077 AN: 10576

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49679 AN: 67964

Other (OTH) AF: 0.727 AC: 1537 AN: 2114

Alfa AF: 0.744 Hom.: 7336

Bravo AF: 0.744

Asia WGS AF: 0.714 AC: 2482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.74
DANN	Benign	0.32
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs1431659; hg19: chr8-73439070;