4-80248758-G-T

Variant names:

• chr4-80248758-G-T
• rs11099098
• XR_007058161.1:n.81-6607G>T

Variant summary

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

The XR_007058161.1(LOC124900725):​n.81-6607G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,978 control chromosomes in the GnomAD database, including 5,137 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 0.23 (5137 hom., cov: 32)
• Consequence: LOC124900725 XR_007058161.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 26 publications found

Genes affected

LOC124900725 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 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: 0.234 AC: 35599 AN: 151860 Hom.: 5138 Cov.: 32

Gnomad AFR AF: 0.0691

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.234 AC: 35595 AN: 151978 Hom.: 5137 Cov.: 32 AF XY: 0.236 AC XY: 17524 AN XY: 74254

African (AFR) AF: 0.0689 AC: 2858 AN: 41482

American (AMR) AF: 0.257 AC: 3917 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 834 AN: 3468

East Asian (EAS) AF: 0.417 AC: 2149 AN: 5158

South Asian (SAS) AF: 0.282 AC: 1359 AN: 4812

European-Finnish (FIN) AF: 0.320 AC: 3365 AN: 10526

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20185 AN: 67954

Other (OTH) AF: 0.229 AC: 483 AN: 2112

Alfa AF: 0.274 Hom.: 9208

Bravo AF: 0.222

Asia WGS AF: 0.320 AC: 1114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.52
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs11099098; hg19: chr4-81169912;