rs2274459

chr6-33794465-G-A

Variant summary

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

The XR_926707.3(LOC105375024):n.3778+1310G>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 0.121 in 152,074 control chromosomes in the GnomAD database, including 1,457 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 0.12 (1457 hom., cov: 32)
• Consequence: LOC105375024 XR_926707.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

Genes affected

LOC105375024 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375024	XR_926707.3	n.3778+1310G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18343 AN: 151956 Hom.: 1456 Cov.: 32

Gnomad AFR AF: 0.0323

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0466

Gnomad SAS AF: 0.0623

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.121 AC: 18349 AN: 152074 Hom.: 1457 Cov.: 32 AF XY: 0.116 AC XY: 8638 AN XY: 74342

Gnomad4 AFR AF: 0.0322

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.0465

Gnomad4 SAS AF: 0.0625

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.150

Alfa AF: 0.164 Hom.: 3109

Bravo AF: 0.122

Asia WGS AF: 0.0600 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	12
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2274459; hg19: chr6-33762242;