XR_942934.2:n.995-478A>G

Variant names:

• chr6-120971903-T-C
• rs9320784
• XR_942934.2:n.995-478A>G

Variant summary

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

The XR_942934.2(LOC105377977):​n.995-478A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 151,572 control chromosomes in the GnomAD database, including 1,615 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 0.13 (1615 hom., cov: 32)
• Consequence: LOC105377977 XR_942934.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160
• Publications: 1 publications found

Genes affected

LOC105377977 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 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: 0.128 AC: 19389 AN: 151454 Hom.: 1614 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0759

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.0559

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0882

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.128 AC: 19414 AN: 151572 Hom.: 1615 Cov.: 32 AF XY: 0.127 AC XY: 9438 AN XY: 74128

African (AFR) AF: 0.228 AC: 9447 AN: 41372

American (AMR) AF: 0.0757 AC: 1147 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3458

East Asian (EAS) AF: 0.108 AC: 556 AN: 5126

South Asian (SAS) AF: 0.197 AC: 951 AN: 4816

European-Finnish (FIN) AF: 0.0559 AC: 593 AN: 10616

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0882 AC: 5977 AN: 67734

Other (OTH) AF: 0.130 AC: 273 AN: 2096

Alfa AF: 0.118 Hom.: 251

Bravo AF: 0.133

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.67
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs9320784; hg19: chr6-121293049;