3-70581456-A-T

Variant names:

• chr3-70581456-A-T
• rs9310194
• XR_001740559.2:n.210-2782T>A

Variant summary

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

The XR_001740559.2(LOC105377152):​n.210-2782T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 151,778 control chromosomes in the GnomAD database, including 4,879 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 0.25 (4879 hom., cov: 31)
• Consequence: LOC105377152 XR_001740559.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 2 publications found

Genes affected

LOC105377152 (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 (EAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377152	XR_001740559.2	n.210-2782T>A		intron_variant	Intron 2 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37183 AN: 151660 Hom.: 4869 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.245 AC: 37231 AN: 151778 Hom.: 4879 Cov.: 31 AF XY: 0.250 AC XY: 18514 AN XY: 74124

African (AFR) AF: 0.225 AC: 9314 AN: 41436

American (AMR) AF: 0.236 AC: 3585 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3470

East Asian (EAS) AF: 0.551 AC: 2830 AN: 5132

South Asian (SAS) AF: 0.382 AC: 1838 AN: 4810

European-Finnish (FIN) AF: 0.285 AC: 3010 AN: 10554

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15201 AN: 67862

Other (OTH) AF: 0.244 AC: 513 AN: 2106

Alfa AF: 0.227 Hom.: 517

Bravo AF: 0.244

Asia WGS AF: 0.447 AC: 1553 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.92
DANN	Benign	0.62
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs9310194; hg19: chr3-70630607;