XR_945388.3:n.119-9936A>G

Variant names:

• chr12-115518350-T-C
• rs7311298
• XR_945388.3:n.119-9936A>G

Variant summary

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

The XR_945388.3(LOC105370003):​n.119-9936A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,210 control chromosomes in the GnomAD database, including 4,012 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 0.16 (4012 hom., cov: 33)
• Consequence: LOC105370003 XR_945388.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.963
• Publications: 0 publications found

Genes affected

LOC105370003 (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 = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370003	XR_945388.3	n.119-9936A>G		intron_variant	Intron 1 of 3
LOC105370003	XR_945389.3	n.119-9936A>G		intron_variant	Intron 1 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24243 AN: 152092 Hom.: 3993 Cov.: 33

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0878

Gnomad ASJ AF: 0.0776

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0244

Gnomad FIN AF: 0.0586

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0498

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.160 AC: 24311 AN: 152210 Hom.: 4012 Cov.: 33 AF XY: 0.155 AC XY: 11555 AN XY: 74434

African (AFR) AF: 0.421 AC: 17465 AN: 41466

American (AMR) AF: 0.0877 AC: 1341 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0776 AC: 269 AN: 3468

East Asian (EAS) AF: 0.148 AC: 770 AN: 5186

South Asian (SAS) AF: 0.0253 AC: 122 AN: 4830

European-Finnish (FIN) AF: 0.0586 AC: 622 AN: 10618

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0499 AC: 3392 AN: 68022

Other (OTH) AF: 0.124 AC: 263 AN: 2116

Alfa AF: 0.0836 Hom.: 4067

Bravo AF: 0.175

Asia WGS AF: 0.113 AC: 393 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	0.24
DANN	Benign	0.39
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs7311298; hg19: chr12-115956155;