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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986667	XR_001744460.3	n.249+30697A>G		intron_variant	Intron 1 of 2

Ensembl

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

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 v4.3

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;