XR_001744460.3:n.249+29511G>A

Variant names:

• chr6-164467333-G-A
• rs2029870
• XR_001744460.3:n.249+29511G>A

Variant summary

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

The XR_001744460.3(LOC107986667):​n.249+29511G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 151,612 control chromosomes in the GnomAD database, including 4,035 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 (4035 hom., cov: 31)
• Consequence: LOC107986667 XR_001744460.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 3 publications found

Genes affected

LOC107986667 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33815 AN: 151496 Hom.: 4025 Cov.: 31

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.223 AC: 33862 AN: 151612 Hom.: 4035 Cov.: 31 AF XY: 0.225 AC XY: 16650 AN XY: 74064

African (AFR) AF: 0.244 AC: 10098 AN: 41310

American (AMR) AF: 0.297 AC: 4509 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 613 AN: 3464

East Asian (EAS) AF: 0.393 AC: 2017 AN: 5132

South Asian (SAS) AF: 0.331 AC: 1594 AN: 4814

European-Finnish (FIN) AF: 0.132 AC: 1376 AN: 10454

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

European-Non Finnish (NFE) AF: 0.191 AC: 12960 AN: 67930

Other (OTH) AF: 0.217 AC: 456 AN: 2106

Alfa AF: 0.207 Hom.: 14668

Bravo AF: 0.235

Asia WGS AF: 0.361 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.2
DANN	Benign	0.62
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs2029870; hg19: chr6-164888366;