4-17660737-A-C

Position:

• chr4-17660737-A-C

Variant summary

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

The NM_015688.2(FAM184B):​c.1695-650T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,096 control chromosomes in the GnomAD database, including 23,431 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 0.53 (23431 hom., cov: 30)
• Consequence: FAM184B NM_015688.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM184B	NM_015688.2	c.1695-650T>G		intron_variant		ENST00000265018.4
FAM184B	XM_047450066.1	c.1695-650T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM184B	ENST00000265018.4	c.1695-650T>G		intron_variant		1	NM_015688.2	P1

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80134 AN: 150980 Hom.: 23419 Cov.: 30

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.531 AC: 80176 AN: 151096 Hom.: 23431 Cov.: 30 AF XY: 0.536 AC XY: 39567 AN XY: 73764

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.566

Alfa AF: 0.553 Hom.: 5453

Bravo AF: 0.518

Asia WGS AF: 0.665 AC: 2313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.71

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: rs9291659; hg19: chr4-17662360;