rs740672

Positions:

• chr4-17780641-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.141+518A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 151,968 control chromosomes in the GnomAD database, including 4,755 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 0.25 (4755 hom., cov: 32)
• Consequence: FAM184B NM_015688.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM184B	NM_015688.2	c.141+518A>G		intron_variant		ENST00000265018.4
FAM184B	XM_047450066.1	c.141+518A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM184B	ENST00000265018.4	c.141+518A>G		intron_variant		1	NM_015688.2	P1

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37484 AN: 151850 Hom.: 4747 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.247 AC: 37517 AN: 151968 Hom.: 4755 Cov.: 32 AF XY: 0.244 AC XY: 18135 AN XY: 74278

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.277

Alfa AF: 0.247 Hom.: 6328

Bravo AF: 0.252

Asia WGS AF: 0.315 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.6
DANN	Benign	0.48

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: rs740672; hg19: chr4-17782264;