rs9312601

Variant names:

• chr4-176445891-T-A
• rs9312601
• XR_007058376.1:n.912+1893T>A

Variant summary

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

The XR_007058376.1(LOC124900817):​n.912+1893T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 151,960 control chromosomes in the GnomAD database, including 27,998 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 0.60 (27998 hom., cov: 32)
• Consequence: LOC124900817 XR_007058376.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 3 publications found

Genes affected

LOC124900817 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.639 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: 0.602 AC: 91479 AN: 151842 Hom.: 27989 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.602 AC: 91512 AN: 151960 Hom.: 27998 Cov.: 32 AF XY: 0.600 AC XY: 44578 AN XY: 74262

African (AFR) AF: 0.540 AC: 22389 AN: 41436

American (AMR) AF: 0.613 AC: 9356 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2629 AN: 3468

East Asian (EAS) AF: 0.373 AC: 1928 AN: 5166

South Asian (SAS) AF: 0.547 AC: 2636 AN: 4816

European-Finnish (FIN) AF: 0.632 AC: 6674 AN: 10566

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43723 AN: 67936

Other (OTH) AF: 0.609 AC: 1283 AN: 2108

Alfa AF: 0.613 Hom.: 3582

Bravo AF: 0.597

Asia WGS AF: 0.437 AC: 1520 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.7
DANN	Benign	0.80
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs9312601; hg19: chr4-177367042;