3-164184635-C-T

Variant names:

• chr3-164184635-C-T
• rs710848
• XR_001740997.2:n.1103+8873G>A

Variant summary

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

The XR_001740997.2(LOC102724419):​n.1103+8873G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 151,984 control chromosomes in the GnomAD database, including 4,033 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 0.22 (4033 hom., cov: 32)
• Consequence: LOC102724419 XR_001740997.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977
• Publications: 1 publications found

Genes affected

LOC102724419 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.262 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: 0.221 AC: 33628 AN: 151866 Hom.: 4031 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.221 AC: 33633 AN: 151984 Hom.: 4033 Cov.: 32 AF XY: 0.225 AC XY: 16730 AN XY: 74272

African (AFR) AF: 0.138 AC: 5733 AN: 41462

American (AMR) AF: 0.261 AC: 3987 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3468

East Asian (EAS) AF: 0.127 AC: 655 AN: 5170

South Asian (SAS) AF: 0.275 AC: 1322 AN: 4814

European-Finnish (FIN) AF: 0.314 AC: 3307 AN: 10524

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.249 AC: 16949 AN: 67970

Other (OTH) AF: 0.221 AC: 466 AN: 2104

Alfa AF: 0.222 Hom.: 526

Bravo AF: 0.213

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.74
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs710848; hg19: chr3-163902423;