6-164468519-A-G

Variant names:

• chr6-164468519-A-G
• rs9459111
• XR_001744460.3:n.249+30697A>G

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+30697A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,068 control chromosomes in the GnomAD database, including 4,596 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 0.24 (4596 hom., cov: 32)
• Consequence: LOC107986667 XR_001744460.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741
• Publications: 1 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=-0.96).
• 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: 0.240 AC: 36464 AN: 151950 Hom.: 4586 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.240 AC: 36512 AN: 152068 Hom.: 4596 Cov.: 32 AF XY: 0.241 AC XY: 17893 AN XY: 74326

African (AFR) AF: 0.255 AC: 10589 AN: 41468

American (AMR) AF: 0.309 AC: 4717 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3468

East Asian (EAS) AF: 0.393 AC: 2029 AN: 5164

South Asian (SAS) AF: 0.336 AC: 1616 AN: 4816

European-Finnish (FIN) AF: 0.149 AC: 1576 AN: 10572

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14617 AN: 67986

Other (OTH) AF: 0.229 AC: 483 AN: 2112

Alfa AF: 0.218 Hom.: 3100

Bravo AF: 0.251

Asia WGS AF: 0.363 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.27
DANN	Benign	0.35
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs9459111; hg19: chr6-164889552; COSMIC: COSV69027693;