6-100952189-T-G

Variant names:

• chr6-100952189-T-G
• rs680857
• XR_002956381.2:n.247-10497T>G

Variant summary

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

The XR_002956381.2(LOC107984041):​n.247-10497T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 151,016 control chromosomes in the GnomAD database, including 35,593 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 0.68 (35593 hom., cov: 29)
• Consequence: LOC107984041 XR_002956381.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806
• Publications: 3 publications found

Genes affected

LOC107984041 (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 (NFE) allele frequency at 95% confidence interval = 0.708 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: 0.683 AC: 103129 AN: 150902 Hom.: 35571 Cov.: 29

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.705

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.683 AC: 103199 AN: 151016 Hom.: 35593 Cov.: 29 AF XY: 0.675 AC XY: 49652 AN XY: 73604

African (AFR) AF: 0.671 AC: 27646 AN: 41210

American (AMR) AF: 0.657 AC: 9969 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2592 AN: 3468

East Asian (EAS) AF: 0.583 AC: 2971 AN: 5094

South Asian (SAS) AF: 0.410 AC: 1966 AN: 4790

European-Finnish (FIN) AF: 0.720 AC: 7308 AN: 10156

Middle Eastern (MID) AF: 0.696 AC: 195 AN: 280

European-Non Finnish (NFE) AF: 0.714 AC: 48420 AN: 67850

Other (OTH) AF: 0.669 AC: 1403 AN: 2096

Alfa AF: 0.702 Hom.: 4694

Bravo AF: 0.686

Asia WGS AF: 0.509 AC: 1767 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	3.4
DANN	Benign	0.52
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs680857; hg19: chr6-101400065;