rs7611945

chr3-125958671-C-T

Variant summary

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

The ENST00000466506.1(FBRSL1P1):n.116C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 590,272 control chromosomes in the GnomAD database, including 13,952 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 0.25 (5994 hom., cov: 33)
  • Exomes 𝑓: 0.18 (7958 hom.)
• Consequence: FBRSL1P1 ENST00000466506.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

FBRSL1P1 (HGNC:56500): (FBRSL1 pseudogene 1)

ALG1L1P (HGNC:33721): (ALG1 like 1, pseudogene) Predicted to enable mannosyltransferase activity. Predicted to be involved in protein glycosylation. Predicted to be active in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALG1L1P	NR_171197.1	n.117-24975G>A		intron_variant, non_coding_transcript_variant
ALG1L1P	NR_171196.1	n.117-24975G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FBRSL1P1	ENST00000466506.1	n.116C>T		non_coding_transcript_exon_variant	1/1
ALG1L1P	ENST00000611639.4	n.117-24125G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000692801.1	n.153-24975G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37882 AN: 152032 Hom.: 5986 Cov.: 33

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.0672

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.268

GnomAD4 exome AF: 0.179 AC: 78526 AN: 438122 Hom.: 7958 Cov.: 0 AF XY: 0.176 AC XY: 41778 AN XY: 237350

Gnomad4 AFR exome AF: 0.443

Gnomad4 AMR exome AF: 0.149

Gnomad4 ASJ exome AF: 0.270

Gnomad4 EAS exome AF: 0.0948

Gnomad4 SAS exome AF: 0.122

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.188

Gnomad4 OTH exome AF: 0.210

GnomAD4 genome AF: 0.249 AC: 37915 AN: 152150 Hom.: 5994 Cov.: 33 AF XY: 0.242 AC XY: 17981 AN XY: 74398

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.0668

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.268

Alfa AF: 0.202 Hom.: 5523

Bravo AF: 0.264

Asia WGS AF: 0.139 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	7.0
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7611945; hg19: chr3-125677514;