rs2955587

chr8-8240557-A-Gchr8-8240557-A-T

Variant summary

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

The ENST00000689104.1(ENSG00000291048):n.316-8T>C variant causes a splice region, splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 1,588,812 control chromosomes in the GnomAD database, including 168,559 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 0.39 (14144 hom., cov: 33)
  • Exomes 𝑓: 0.45 (154415 hom.)
• Consequence: ENST00000689104.1 splice_region, splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

Genes affected

ALG1L13P (HGNC:44382): (ALG1 like 13, pseudogene)

FAM86B3P (HGNC:44371): (family with sequence similarity 86 member B3, pseudogene)

(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 (EAS) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM86B3P	NR_024361.1	n.929+3282A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALG1L13P	ENST00000519320.1	n.117-9T>C		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant
FAM86B3P	ENST00000522601.5	n.904+3282A>G		intron_variant, non_coding_transcript_variant		1
	ENST00000689104.1	n.316-8T>C		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58820 AN: 151940 Hom.: 14135 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.384

GnomAD4 exome AF: 0.453 AC: 651310 AN: 1436754 Hom.: 154415 Cov.: 41 AF XY: 0.452 AC XY: 323039 AN XY: 714826

Gnomad4 AFR exome AF: 0.0982

Gnomad4 AMR exome AF: 0.694

Gnomad4 ASJ exome AF: 0.315

Gnomad4 EAS exome AF: 0.810

Gnomad4 SAS exome AF: 0.453

Gnomad4 FIN exome AF: 0.578

Gnomad4 NFE exome AF: 0.441

Gnomad4 OTH exome AF: 0.432

GnomAD4 genome AF: 0.387 AC: 58840 AN: 152058 Hom.: 14144 Cov.: 33 AF XY: 0.400 AC XY: 29770 AN XY: 74350

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.386

Alfa AF: 0.423 Hom.: 6272

Bravo AF: 0.380

Asia WGS AF: 0.560 AC: 1944 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	0.85
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2955587; hg19: chr8-8098079;