chr7-108822214-T-C

Variant names:

• chr7-108822214-T-C
• rs940720
• XR_001745322.1:n.378-18443T>C

Variant summary

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

The XR_001745322.1(LOC107986836):​n.378-18443T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.956 in 152,136 control chromosomes in the GnomAD database, including 69,894 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 0.96 (69894 hom., cov: 30)
• Consequence: LOC107986836 XR_001745322.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 0 publications found

Genes affected

LOC107986836 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.956 AC: 145397 AN: 152018 Hom.: 69850 Cov.: 30

Gnomad AFR AF: 0.850

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.982

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.966

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

GnomAD4 genome AF: 0.956 AC: 145501 AN: 152136 Hom.: 69894 Cov.: 30 AF XY: 0.958 AC XY: 71238 AN XY: 74366

African (AFR) AF: 0.850 AC: 35272 AN: 41478

American (AMR) AF: 0.982 AC: 14990 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3469 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5151 AN: 5152

South Asian (SAS) AF: 1.00 AC: 4813 AN: 4814

European-Finnish (FIN) AF: 1.00 AC: 10606 AN: 10608

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67959 AN: 68020

Other (OTH) AF: 0.966 AC: 2042 AN: 2114

Alfa AF: 0.972 Hom.: 24962

Bravo AF: 0.951

Asia WGS AF: 0.992 AC: 3446 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.91
DANN	Benign	0.63
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs940720; hg19: chr7-108462658;