rs9291659

Variant names:

• chr4-17660737-A-C
• rs9291659
• NM_015688.2:c.1695-650T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-17660737-A-C
• chr4-17660737-A-G
• chr4-17660737-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FAM184B	NM_015688.2	c.1695-650T>G		intron_variant	Intron 8 of 17	ENST00000265018.4	NP_056503.1
FAM184B	XM_047450066.1	c.1695-650T>G		intron_variant	Intron 8 of 16		XP_047306022.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM184B	ENST00000265018.4	c.1695-650T>G		intron_variant	Intron 8 of 17	1	NM_015688.2	ENSP00000265018.3

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

African (AFR) AF: 0.275 AC: 11237 AN: 40834

American (AMR) AF: 0.659 AC: 9999 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1792 AN: 3462

East Asian (EAS) AF: 0.826 AC: 4251 AN: 5148

South Asian (SAS) AF: 0.549 AC: 2631 AN: 4788

European-Finnish (FIN) AF: 0.681 AC: 7134 AN: 10474

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41260 AN: 67912

Other (OTH) AF: 0.566 AC: 1187 AN: 2096

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
PhyloP100		0.19
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9291659; hg19: chr4-17662360;