rs2408954

chr12-48028706-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001749115.3(LOC105369750):n.227-1065G>A 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 0.279 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50

Genes affected

LOC105369750 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105369750	XR_001749115.3	n.227-1065G>A		intron_variant, non_coding_transcript_variant
LOC105369750	XR_001749116.3	n.168-1065G>A		intron_variant, non_coding_transcript_variant
LOC105369750	XR_944904.3	n.227-1065G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.245

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2408954; hg19: chr12-48422489;