chr17-39572778-C-T

Variant names:

• chr17-39572778-C-T
• rs1874226
• XR_934745.3:n.203+150G>A

Variant summary

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

The XR_934745.3(LOC105371770):​n.203+150G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 151,940 control chromosomes in the GnomAD database, including 4,379 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 0.22 (4379 hom., cov: 31)
• Consequence: LOC105371770 XR_934745.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657
• Publications: 13 publications found

Genes affected

LOC105371770 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 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: 0.221 AC: 33539 AN: 151822 Hom.: 4378 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.0814

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.221 AC: 33574 AN: 151940 Hom.: 4379 Cov.: 31 AF XY: 0.218 AC XY: 16171 AN XY: 74250

African (AFR) AF: 0.355 AC: 14693 AN: 41374

American (AMR) AF: 0.252 AC: 3846 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 811 AN: 3468

East Asian (EAS) AF: 0.240 AC: 1239 AN: 5160

South Asian (SAS) AF: 0.0821 AC: 396 AN: 4822

European-Finnish (FIN) AF: 0.0817 AC: 866 AN: 10602

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11003 AN: 67954

Other (OTH) AF: 0.216 AC: 457 AN: 2116

Alfa AF: 0.188 Hom.: 404

Bravo AF: 0.244

Asia WGS AF: 0.149 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.74
DANN	Benign	0.55
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs1874226; hg19: chr17-37729031;