3-104387859-A-G

Variant names:

• chr3-104387859-A-G
• rs2398966
• XR_924301.3:n.166-26528T>C

Variant summary

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

The XR_924301.3(LOC105374020):​n.166-26528T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,194 control chromosomes in the GnomAD database, including 19,361 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 0.49 (19361 hom., cov: 31)
• Consequence: LOC105374020 XR_924301.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.50
• Publications: 2 publications found

Genes affected

LOC105374020 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 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: 0.493 AC: 74415 AN: 151076 Hom.: 19362 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.492 AC: 74414 AN: 151194 Hom.: 19361 Cov.: 31 AF XY: 0.487 AC XY: 36020 AN XY: 73900

African (AFR) AF: 0.355 AC: 14667 AN: 41352

American (AMR) AF: 0.477 AC: 7215 AN: 15132

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1964 AN: 3426

East Asian (EAS) AF: 0.190 AC: 979 AN: 5142

South Asian (SAS) AF: 0.457 AC: 2201 AN: 4816

European-Finnish (FIN) AF: 0.542 AC: 5707 AN: 10536

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.591 AC: 39887 AN: 67504

Other (OTH) AF: 0.506 AC: 1060 AN: 2094

Alfa AF: 0.555 Hom.: 12156

Bravo AF: 0.477

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.39
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs2398966; hg19: chr3-104106703;