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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376637	XR_001748194.1	n.58+34803T>C		intron_variant	Intron 1 of 3
LOC105376637	XR_001748195.2	n.58+34803T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;