4-17681211-T-C

Variant summary

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

The NM_015688.2(FAM184B):c.1596+7213A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 152,090 control chromosomes in the GnomAD database, including 25,008 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 0.56 (25008 hom., cov: 33)
• Consequence: FAM184B NM_015688.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.967

Genes affected

FAM184B (HGNC:29235): (family with sequence similarity 184 member B)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM184B	NM_015688.2	c.1596+7213A>G		intron_variant		ENST00000265018.4
FAM184B	XM_047450066.1	c.1596+7213A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM184B	ENST00000265018.4	c.1596+7213A>G		intron_variant		1	NM_015688.2	P1

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84771 AN: 151972 Hom.: 24986 Cov.: 33

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.582

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.558 AC: 84835 AN: 152090 Hom.: 25008 Cov.: 33 AF XY: 0.563 AC XY: 41898 AN XY: 74360

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.586

Alfa AF: 0.602 Hom.: 27091

Bravo AF: 0.550

Asia WGS AF: 0.691 AC: 2404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	9.3
Dann	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1008375; hg19: chr4-17682834;