XR_001746877.2:n.841+6222C>G

Variant names:

• chr9-107599719-C-G
• rs6477578
• XR_001746877.2:n.841+6222C>G

Variant summary

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

The XR_001746877.2(LOC105376205):​n.841+6222C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,968 control chromosomes in the GnomAD database, including 10,664 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 0.35 (10664 hom., cov: 32)
• Consequence: LOC105376205 XR_001746877.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400
• Publications: 2 publications found

Genes affected

LOC105376205 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 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: 0.350 AC: 53085 AN: 151850 Hom.: 10617 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.350 AC: 53192 AN: 151968 Hom.: 10664 Cov.: 32 AF XY: 0.345 AC XY: 25609 AN XY: 74262

African (AFR) AF: 0.554 AC: 22936 AN: 41436

American (AMR) AF: 0.349 AC: 5329 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1187 AN: 3468

East Asian (EAS) AF: 0.336 AC: 1728 AN: 5148

South Asian (SAS) AF: 0.250 AC: 1204 AN: 4824

European-Finnish (FIN) AF: 0.182 AC: 1924 AN: 10564

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17705 AN: 67934

Other (OTH) AF: 0.354 AC: 750 AN: 2116

Alfa AF: 0.310 Hom.: 1053

Bravo AF: 0.372

Asia WGS AF: 0.395 AC: 1373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.64
DANN	Benign	0.43
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs6477578; hg19: chr9-110362000;