rs674546

Positions:

• chr11-102859908-A-G
• chr11-102859908-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007062868.1(LOC124902741):​n.1991+4125A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,050 control chromosomes in the GnomAD database, including 4,460 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 (4460 hom., cov: 32)
• Consequence: LOC124902741 XR_007062868.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

Genes affected

LOC124902741 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902741	XR_007062868.1	n.1991+4125A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34873 AN: 151930 Hom.: 4454 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.229 AC: 34891 AN: 152050 Hom.: 4460 Cov.: 32 AF XY: 0.228 AC XY: 16949 AN XY: 74312

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.220

Alfa AF: 0.207 Hom.: 448

Bravo AF: 0.227

Asia WGS AF: 0.173 AC: 601 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.69
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs674546; hg19: chr11-102730639;