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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900725	XR_007058161.1	n.81-6607G>T		intron_variant	Intron 1 of 1

Ensembl

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

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 v4.3

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;