22-46047955-C-T

Variant summary

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

The XM_047441696.1(LOC124905135):c.-5555+2948C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,124 control chromosomes in the GnomAD database, including 23,671 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 0.52 (23671 hom., cov: 33)
• Consequence: LOC124905135 XM_047441696.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

Genes affected

LOC124905135 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124905135	XM_047441696.1	c.-5555+2948C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000692935.1	n.234+224G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78342 AN: 152006 Hom.: 23618 Cov.: 33

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.516 AC: 78434 AN: 152124 Hom.: 23671 Cov.: 33 AF XY: 0.504 AC XY: 37459 AN XY: 74360

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.481

Alfa AF: 0.403 Hom.: 6978

Bravo AF: 0.536

Asia WGS AF: 0.267 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.12
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: rs8137243; hg19: chr22-46443835;