rs2408954

Variant names:

• chr12-48028706-G-A
• rs2408954
• XR_001749115.3:n.227-1065G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001749115.3(LOC105369750):​n.227-1065G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,004 control chromosomes in the GnomAD database, including 7,254 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 0.28 (7254 hom., cov: 31)
• Consequence: LOC105369750 XR_001749115.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 2 publications found

Genes affected

LOC105369750 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369750	XR_001749115.3	n.227-1065G>A		intron_variant	Intron 2 of 2
LOC105369750	XR_001749116.3	n.168-1065G>A		intron_variant	Intron 2 of 2
LOC105369750	XR_944904.3	n.227-1065G>A		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42412 AN: 151886 Hom.: 7249 Cov.: 31

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.279 AC: 42453 AN: 152004 Hom.: 7254 Cov.: 31 AF XY: 0.276 AC XY: 20520 AN XY: 74312

African (AFR) AF: 0.480 AC: 19878 AN: 41408

American (AMR) AF: 0.163 AC: 2494 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3470

East Asian (EAS) AF: 0.158 AC: 817 AN: 5172

South Asian (SAS) AF: 0.150 AC: 723 AN: 4816

European-Finnish (FIN) AF: 0.255 AC: 2700 AN: 10568

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14536 AN: 67976

Other (OTH) AF: 0.245 AC: 517 AN: 2110

Alfa AF: 0.261 Hom.: 802

Bravo AF: 0.282

Asia WGS AF: 0.177 AC: 615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	18
DANN	Benign	0.87
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs2408954; hg19: chr12-48422489;