4-17735633-T-C

Position:

• chr4-17735633-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.142-25989A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 150,582 control chromosomes in the GnomAD database, including 6,118 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 0.28 (6118 hom., cov: 31)
• Consequence: FAM184B NM_015688.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM184B	NM_015688.2	c.142-25989A>G		intron_variant		ENST00000265018.4
FAM184B	XM_047450066.1	c.142-25989A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM184B	ENST00000265018.4	c.142-25989A>G		intron_variant		1	NM_015688.2	P1

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42164 AN: 150464 Hom.: 6117 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.321

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.280 AC: 42178 AN: 150582 Hom.: 6118 Cov.: 31 AF XY: 0.272 AC XY: 20054 AN XY: 73642

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.301

Alfa AF: 0.291 Hom.: 814

Bravo AF: 0.284

Asia WGS AF: 0.217 AC: 755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.42

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: rs13104297; hg19: chr4-17737256;