chr6-100947531-G-A

Variant names:

• chr6-100947531-G-A
• rs11969893
• XR_002956381.2:n.247-15155G>A

Variant summary

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

The XR_002956381.2(LOC107984041):​n.247-15155G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0376 in 152,112 control chromosomes in the GnomAD database, including 138 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 0.038 (138 hom., cov: 31)
• Consequence: LOC107984041 XR_002956381.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 10 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0549 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: 0.0376 AC: 5711 AN: 151994 Hom.: 137 Cov.: 31

Gnomad AFR AF: 0.0569

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.00893

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.0155

Gnomad FIN AF: 0.0483

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0324

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0376 AC: 5717 AN: 152112 Hom.: 138 Cov.: 31 AF XY: 0.0369 AC XY: 2746 AN XY: 74364

African (AFR) AF: 0.0569 AC: 2359 AN: 41492

American (AMR) AF: 0.0272 AC: 415 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00893 AC: 31 AN: 3470

East Asian (EAS) AF: 0.000969 AC: 5 AN: 5162

South Asian (SAS) AF: 0.0156 AC: 75 AN: 4822

European-Finnish (FIN) AF: 0.0483 AC: 511 AN: 10576

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0324 AC: 2202 AN: 67992

Other (OTH) AF: 0.0397 AC: 84 AN: 2114

Alfa AF: 0.0305 Hom.: 222

Bravo AF: 0.0368

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.49
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs11969893; hg19: chr6-101395407;