XR_942986.3:n.778+4422T>C

Variant names:

• chr6-129942446-T-C
• rs9375683
• XR_942986.3:n.778+4422T>C

Variant summary

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

The XR_942986.3(LOC105377999):​n.778+4422T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,118 control chromosomes in the GnomAD database, including 4,136 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 0.23 (4136 hom., cov: 32)
• Consequence: LOC105377999 XR_942986.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454
• Publications: 4 publications found

Genes affected

LOC105377999 (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 (AMR) allele frequency at 95% confidence interval = 0.309 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: 0.225 AC: 34242 AN: 152000 Hom.: 4120 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.225 AC: 34273 AN: 152118 Hom.: 4136 Cov.: 32 AF XY: 0.230 AC XY: 17140 AN XY: 74362

African (AFR) AF: 0.168 AC: 6979 AN: 41524

American (AMR) AF: 0.316 AC: 4832 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 580 AN: 3468

East Asian (EAS) AF: 0.290 AC: 1501 AN: 5174

South Asian (SAS) AF: 0.241 AC: 1159 AN: 4818

European-Finnish (FIN) AF: 0.290 AC: 3059 AN: 10558

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.226 AC: 15342 AN: 67988

Other (OTH) AF: 0.246 AC: 519 AN: 2112

Alfa AF: 0.227 Hom.: 6747

Bravo AF: 0.225

Asia WGS AF: 0.280 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.7
DANN	Benign	0.77
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs9375683; hg19: chr6-130263591;