rs1444067

Variant names:

• chr18-65503450-G-T
• rs1444067
• XR_935583.2:n.117+3106C>A

Variant summary

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

The XR_935583.2(LOC105372169):​n.117+3106C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 150,972 control chromosomes in the GnomAD database, including 16,459 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 0.46 (16459 hom., cov: 32)
• Consequence: LOC105372169 XR_935583.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 4 publications found

Genes affected

LOC105372169 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 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: 0.464 AC: 70063 AN: 150854 Hom.: 16443 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.464 AC: 70121 AN: 150972 Hom.: 16459 Cov.: 32 AF XY: 0.463 AC XY: 34197 AN XY: 73786

African (AFR) AF: 0.511 AC: 21146 AN: 41360

American (AMR) AF: 0.405 AC: 6124 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1943 AN: 3444

East Asian (EAS) AF: 0.594 AC: 3057 AN: 5144

South Asian (SAS) AF: 0.465 AC: 2239 AN: 4818

European-Finnish (FIN) AF: 0.403 AC: 4253 AN: 10546

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 29732 AN: 67250

Other (OTH) AF: 0.456 AC: 957 AN: 2100

Alfa AF: 0.447 Hom.: 2607

Bravo AF: 0.472

Asia WGS AF: 0.461 AC: 1597 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.40
DANN	Benign	0.63
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1444067; hg19: chr18-63170686;