rs1026604

Variant names:

• chr11-39928358-A-G
• rs1026604
• XR_001748194.1:n.58+34803T>C

Variant summary

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

The XR_001748194.1(LOC105376637):​n.58+34803T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,002 control chromosomes in the GnomAD database, including 3,850 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 (3850 hom., cov: 31)
• Consequence: LOC105376637 XR_001748194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• Publications: 2 publications found

Genes affected

LOC105376637 (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 = 0.287 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: 0.217 AC: 33009 AN: 151884 Hom.: 3847 Cov.: 31

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.217 AC: 33035 AN: 152002 Hom.: 3850 Cov.: 31 AF XY: 0.214 AC XY: 15877 AN XY: 74314

African (AFR) AF: 0.291 AC: 12067 AN: 41426

American (AMR) AF: 0.175 AC: 2672 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 909 AN: 3472

East Asian (EAS) AF: 0.154 AC: 794 AN: 5158

South Asian (SAS) AF: 0.139 AC: 671 AN: 4822

European-Finnish (FIN) AF: 0.153 AC: 1616 AN: 10570

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13547 AN: 67968

Other (OTH) AF: 0.243 AC: 514 AN: 2114

Alfa AF: 0.211 Hom.: 491

Bravo AF: 0.222

Asia WGS AF: 0.174 AC: 606 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.51
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1026604; hg19: chr11-39949908;