rs1407850

Variant names:

• chr9-108302521-C-T
• rs1407850
• XR_001746881.2:n.720+8145G>A

Variant summary

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

The XR_001746881.2(LOC105376214):​n.720+8145G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 152,108 control chromosomes in the GnomAD database, including 32,347 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 0.64 (32347 hom., cov: 33)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 4 publications found

Genes affected

LOC105376214 (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 (AFR) allele frequency at 95% confidence interval = 0.833 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: 0.638 AC: 96945 AN: 151990 Hom.: 32284 Cov.: 33

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.638 AC: 97068 AN: 152108 Hom.: 32347 Cov.: 33 AF XY: 0.632 AC XY: 46968 AN XY: 74334

African (AFR) AF: 0.841 AC: 34911 AN: 41526

American (AMR) AF: 0.656 AC: 10028 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2237 AN: 3470

East Asian (EAS) AF: 0.594 AC: 3065 AN: 5164

South Asian (SAS) AF: 0.436 AC: 2099 AN: 4812

European-Finnish (FIN) AF: 0.480 AC: 5062 AN: 10556

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37757 AN: 67976

Other (OTH) AF: 0.635 AC: 1337 AN: 2106

Alfa AF: 0.605 Hom.: 9267

Bravo AF: 0.659

Asia WGS AF: 0.551 AC: 1916 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	0.20
DANN	Benign	0.16
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1407850; hg19: chr9-111064801; COSMIC: COSV60390796;