chr6-18498297-T-G

Variant names:

• chr6-18498297-T-G
• rs1359339
• XR_926548.3:n.147+1291T>G

Variant summary

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

The XR_926548.3(LOC105374955):​n.147+1291T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 152,178 control chromosomes in the GnomAD database, including 54,158 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 0.84 (54158 hom., cov: 32)
• Consequence: LOC105374955 XR_926548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 3 publications found

Genes affected

LOC105374955 (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 (AFR) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127695 AN: 152062 Hom.: 54099 Cov.: 32

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.840 AC: 127811 AN: 152178 Hom.: 54158 Cov.: 32 AF XY: 0.833 AC XY: 61905 AN XY: 74358

African (AFR) AF: 0.961 AC: 39931 AN: 41564

American (AMR) AF: 0.807 AC: 12345 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2769 AN: 3472

East Asian (EAS) AF: 0.888 AC: 4567 AN: 5144

South Asian (SAS) AF: 0.731 AC: 3525 AN: 4824

European-Finnish (FIN) AF: 0.748 AC: 7908 AN: 10570

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.797 AC: 54201 AN: 67992

Other (OTH) AF: 0.837 AC: 1770 AN: 2114

Alfa AF: 0.768 Hom.: 2509

Bravo AF: 0.855

Asia WGS AF: 0.825 AC: 2867 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	0.047
DANN	Benign	0.51
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1359339; hg19: chr6-18498528;