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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374433	XR_925266.3	n.202+2209C>A		intron_variant	Intron 1 of 3
LOC105374433	XR_925267.3	n.202+2209C>A		intron_variant	Intron 1 of 2
LOC105374434	XR_925268.1	n.144-10452G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;