rs4380275

chr2-773278-C-T

Variant summary

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

The XR_007086128.1(LOC105373480):n.807-3558C>T 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 0.719 in 152,118 control chromosomes in the GnomAD database, including 39,940 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 0.72 (39940 hom., cov: 33)
• Consequence: LOC105373480 XR_007086128.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

Genes affected

LOC105373480 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373480	XR_007086128.1	n.807-3558C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109213 AN: 151998 Hom.: 39881 Cov.: 33

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.719 AC: 109335 AN: 152118 Hom.: 39940 Cov.: 33 AF XY: 0.720 AC XY: 53512 AN XY: 74350

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.699

Alfa AF: 0.650 Hom.: 65587

Bravo AF: 0.728

Asia WGS AF: 0.772 AC: 2685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.9
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4380275; hg19: chr2-773278;