8-8237303-T-C

Variant names:

• chr8-8237303-T-C
• rs2980438
• ENST00000522601.5:n.904+28T>C

Variant summary

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

The ENST00000522601.5(FAM86B3P):​n.904+28T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 1,125,304 control chromosomes in the GnomAD database, including 186,565 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 0.59 (27126 hom., cov: 33)
  • Exomes 𝑓: 0.57 (159439 hom.)
• Consequence: FAM86B3P ENST00000522601.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 9 publications found

Genes affected

FAM86B3P (HGNC:):

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

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

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALG1L13P		n.8237303T>C		intragenic_variant
FAM86B3P	NR_024361.1	n.929+28T>C		intron_variant	Intron 7 of 8
FAM86B3P	NR_024362.1	n.1026+28T>C		intron_variant	Intron 7 of 7
FAM86B3P	NR_024363.1	n.656+28T>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM86B3P	ENST00000522601.5	n.904+28T>C		intron_variant	Intron 7 of 8	1
FAM86B3P	ENST00000588728.5	n.626+28T>C		intron_variant	Intron 5 of 5	1
FAM85B	ENST00000834326.1	n.891A>G		non_coding_transcript_exon_variant	Exon 7 of 7

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89424 AN: 151988 Hom.: 27084 Cov.: 33

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.565

GnomAD4 exome AF: 0.569 AC: 553897 AN: 973198 Hom.: 159439 Cov.: 14 AF XY: 0.567 AC XY: 285578 AN XY: 503960

African (AFR) AF: 0.649 AC: 15811 AN: 24352

American (AMR) AF: 0.758 AC: 32471 AN: 42812

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 9635 AN: 22250

East Asian (EAS) AF: 0.889 AC: 30297 AN: 34078

South Asian (SAS) AF: 0.625 AC: 48331 AN: 77316

European-Finnish (FIN) AF: 0.602 AC: 23245 AN: 38590

Middle Eastern (MID) AF: 0.538 AC: 1733 AN: 3224

European-Non Finnish (NFE) AF: 0.536 AC: 368067 AN: 687280

Other (OTH) AF: 0.561 AC: 24307 AN: 43296

GnomAD4 genome AF: 0.589 AC: 89526 AN: 152106 Hom.: 27126 Cov.: 33 AF XY: 0.599 AC XY: 44529 AN XY: 74352

African (AFR) AF: 0.644 AC: 26732 AN: 41494

American (AMR) AF: 0.683 AC: 10430 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1503 AN: 3472

East Asian (EAS) AF: 0.895 AC: 4637 AN: 5180

South Asian (SAS) AF: 0.631 AC: 3037 AN: 4816

European-Finnish (FIN) AF: 0.633 AC: 6693 AN: 10578

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34617 AN: 67970

Other (OTH) AF: 0.570 AC: 1202 AN: 2110

Alfa AF: 0.532 Hom.: 2843

Bravo AF: 0.599

Asia WGS AF: 0.743 AC: 2581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.40
PhyloP100		-1.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2980438; hg19: chr8-8094825;