rs2980438

Positions:

• chr8-8237303-T-C
• chr8-8237303-T-G

Variant summary

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

The NR_024361.1(FAM86B3P):​n.929+28T>C variant causes a intron, non coding transcript 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 NR_024361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

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=-0.92).
• 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/exons	MANE	UniProt
FAM86B3P	NR_024361.1	n.929+28T>C		intron_variant, non_coding_transcript_variant
FAM86B3P	NR_024362.1	n.1026+28T>C		intron_variant, non_coding_transcript_variant
FAM86B3P	NR_024363.1	n.656+28T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM86B3P	ENST00000522601.5	n.904+28T>C		intron_variant, non_coding_transcript_variant		1
	ENST00000689104.1	n.608-501A>G		intron_variant, non_coding_transcript_variant
FAM86B3P	ENST00000523992.2			downstream_gene_variant

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

Gnomad4 AFR exome AF: 0.649

Gnomad4 AMR exome AF: 0.758

Gnomad4 ASJ exome AF: 0.433

Gnomad4 EAS exome AF: 0.889

Gnomad4 SAS exome AF: 0.625

Gnomad4 FIN exome AF: 0.602

Gnomad4 NFE exome AF: 0.536

Gnomad4 OTH exome AF: 0.561

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

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.570

Alfa AF: 0.527 Hom.: 2685

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
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2980438; hg19: chr8-8094825;