rs2955587

Variant names:

• chr8-8240557-A-G
• rs2955587
• ENST00000522601.5:n.904+3282A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-8240557-A-G
• chr8-8240557-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522601.5(FAM86B3P):​n.904+3282A>G variant causes a intron 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: FAM86B3P ENST00000522601.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 12 publications found

Genes affected

FAM86B3P (HGNC:):

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

FAM85B (HGNC:32160): (family with sequence similarity 85 member B)

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ALG1L13P		n.8240557A>G		intragenic_variant
FAM86B3P	NR_024361.1	n.929+3282A>G		intron_variant	Intron 7 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM86B3P	ENST00000522601.5	n.904+3282A>G		intron_variant	Intron 7 of 8	1
FAM86B3P	ENST00000310542.3	n.189A>G		non_coding_transcript_exon_variant	Exon 1 of 2	2
ALG1L13P	ENST00000519320.1	n.117-9T>C		intron_variant	Intron 1 of 4	6

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

African (AFR) AF: 0.0982 AC: 3238 AN: 32974

American (AMR) AF: 0.694 AC: 30425 AN: 43840

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 8060 AN: 25612

East Asian (EAS) AF: 0.810 AC: 31789 AN: 39260

South Asian (SAS) AF: 0.453 AC: 38791 AN: 85610

European-Finnish (FIN) AF: 0.578 AC: 29939 AN: 51802

Middle Eastern (MID) AF: 0.344 AC: 1558 AN: 4526

European-Non Finnish (NFE) AF: 0.441 AC: 481981 AN: 1094094

Other (OTH) AF: 0.432 AC: 25529 AN: 59036

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

African (AFR) AF: 0.115 AC: 4768 AN: 41514

American (AMR) AF: 0.571 AC: 8738 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3470

East Asian (EAS) AF: 0.798 AC: 4103 AN: 5142

South Asian (SAS) AF: 0.471 AC: 2273 AN: 4822

European-Finnish (FIN) AF: 0.601 AC: 6356 AN: 10576

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30118 AN: 67934

Other (OTH) AF: 0.386 AC: 814 AN: 2108

Alfa AF: 0.395 Hom.: 11482

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
PhyloP100		-0.037

Splicing

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

Other links and lift over

dbSNP: rs2955587; hg19: chr8-8098079;