rs2006970

Variant names:

• chr4-43318490-C-A
• rs2006970
• XR_925266.3:n.202+2209C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-43318490-C-A
• chr4-43318490-C-G
• chr4-43318490-C-T

Variant summary

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

The XR_925266.3(LOC105374433):​n.202+2209C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 152,074 control chromosomes in the GnomAD database, including 22,002 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 0.52 (22002 hom., cov: 34)
• Consequence: LOC105374433 XR_925266.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• Publications: 0 publications found

Genes affected

LOC105374433 (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 = 0.64 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: 0.519 AC: 78802 AN: 151956 Hom.: 22009 Cov.: 34

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.518 AC: 78801 AN: 152074 Hom.: 22002 Cov.: 34 AF XY: 0.509 AC XY: 37862 AN XY: 74338

African (AFR) AF: 0.351 AC: 14560 AN: 41478

American (AMR) AF: 0.500 AC: 7633 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1777 AN: 3470

East Asian (EAS) AF: 0.175 AC: 909 AN: 5184

South Asian (SAS) AF: 0.456 AC: 2201 AN: 4824

European-Finnish (FIN) AF: 0.556 AC: 5876 AN: 10562

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.645 AC: 43853 AN: 67978

Other (OTH) AF: 0.533 AC: 1126 AN: 2114

Alfa AF: 0.573 Hom.: 3406

Bravo AF: 0.508

Asia WGS AF: 0.314 AC: 1095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.62
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs2006970; hg19: chr4-43320507;