chr3-106570103-T-C

Variant names:

• chr3-106570103-T-C
• rs12491921
• XR_007095992.1:n.758-11317A>G

Variant summary

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

The XR_007095992.1(LOC101929485):​n.758-11317A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,700 control chromosomes in the GnomAD database, including 14,762 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 0.44 (14762 hom., cov: 30)
• Consequence: LOC101929485 XR_007095992.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799
• Publications: 9 publications found

Genes affected

LOC101929485 (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 (NFE) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929485	XR_007095992.1	n.758-11317A>G		intron_variant	Intron 2 of 15

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66021 AN: 151576 Hom.: 14760 Cov.: 30

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.435 AC: 66054 AN: 151700 Hom.: 14762 Cov.: 30 AF XY: 0.434 AC XY: 32159 AN XY: 74072

African (AFR) AF: 0.367 AC: 15180 AN: 41416

American (AMR) AF: 0.416 AC: 6340 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1799 AN: 3464

East Asian (EAS) AF: 0.266 AC: 1339 AN: 5028

South Asian (SAS) AF: 0.356 AC: 1704 AN: 4784

European-Finnish (FIN) AF: 0.482 AC: 5086 AN: 10550

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.488 AC: 33139 AN: 67912

Other (OTH) AF: 0.439 AC: 928 AN: 2112

Alfa AF: 0.468 Hom.: 57230

Bravo AF: 0.426

Asia WGS AF: 0.296 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.88
DANN	Benign	0.58
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs12491921; hg19: chr3-106288950;