chr3-55150186-C-G

Variant names:

• chr3-55150186-C-G
• rs6782380
• XR_007095917.1:n.159-6264G>C

Variant summary

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

The XR_007095917.1(LOC124906243):​n.159-6264G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,056 control chromosomes in the GnomAD database, including 2,222 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 0.17 (2222 hom., cov: 33)
• Consequence: LOC124906243 XR_007095917.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 5 publications found

Genes affected

LOC124906243 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 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: 0.168 AC: 25520 AN: 151938 Hom.: 2215 Cov.: 33

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.0978

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.168 AC: 25566 AN: 152056 Hom.: 2222 Cov.: 33 AF XY: 0.162 AC XY: 12067 AN XY: 74302

African (AFR) AF: 0.203 AC: 8408 AN: 41488

American (AMR) AF: 0.121 AC: 1838 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 752 AN: 3468

East Asian (EAS) AF: 0.0982 AC: 507 AN: 5164

South Asian (SAS) AF: 0.132 AC: 637 AN: 4828

European-Finnish (FIN) AF: 0.120 AC: 1268 AN: 10564

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11642 AN: 67982

Other (OTH) AF: 0.177 AC: 374 AN: 2110

Alfa AF: 0.162 Hom.: 265

Bravo AF: 0.171

Asia WGS AF: 0.129 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.35
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6782380; hg19: chr3-55184213;