3-188022735-T-C

Variant names:

• chr3-188022735-T-C
• rs6808574
• XR_001741061.2:n.163-18747A>G

Variant summary

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

The XR_001741061.2(LOC107986166):​n.163-18747A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 152,102 control chromosomes in the GnomAD database, including 34,725 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 0.67 (34725 hom., cov: 32)
• Consequence: LOC107986166 XR_001741061.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 55 publications found

Genes affected

LOC107986166 (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 (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101757 AN: 151984 Hom.: 34681 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.670 AC: 101856 AN: 152102 Hom.: 34725 Cov.: 32 AF XY: 0.676 AC XY: 50243 AN XY: 74362

African (AFR) AF: 0.710 AC: 29443 AN: 41468

American (AMR) AF: 0.733 AC: 11206 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2166 AN: 3470

East Asian (EAS) AF: 0.995 AC: 5151 AN: 5178

South Asian (SAS) AF: 0.789 AC: 3813 AN: 4832

European-Finnish (FIN) AF: 0.604 AC: 6383 AN: 10564

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41732 AN: 67990

Other (OTH) AF: 0.665 AC: 1404 AN: 2112

Alfa AF: 0.639 Hom.: 98472

Bravo AF: 0.679

Asia WGS AF: 0.885 AC: 3075 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	3.8
DANN	Benign	0.53
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs6808574; hg19: chr3-187740523; COSMIC: COSV55129687;