17-49721363-A-G

Variant names:

• chr17-49721363-A-G
• rs7225566
• NM_030802.4:c.463-927T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030802.4(FAM117A):​c.463-927T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 152,226 control chromosomes in the GnomAD database, including 61,137 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 0.90 (61137 hom., cov: 31)
• Consequence: FAM117A NM_030802.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.559
• Publications: 6 publications found

Genes affected

FAM117A (HGNC:24179): (family with sequence similarity 117 member A)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030802.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM117A	NM_030802.4	MANE Select	c.463-927T>C		intron	N/A	NP_110429.1
	FAM117A	NM_001411126.1		c.-354-927T>C		intron	N/A	NP_001398055.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM117A	ENST00000240364.7	TSL:1 MANE Select	c.463-927T>C		intron	N/A	ENSP00000240364.2
	FAM117A	ENST00000511743.5	TSL:3	c.133-927T>C		intron	N/A	ENSP00000427326.1
	FAM117A	ENST00000506156.1	TSL:3	c.367-927T>C		intron	N/A	ENSP00000421412.1

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136223 AN: 152108 Hom.: 61076 Cov.: 31

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.896 AC: 136341 AN: 152226 Hom.: 61137 Cov.: 31 AF XY: 0.897 AC XY: 66788 AN XY: 74438

African (AFR) AF: 0.923 AC: 38341 AN: 41536

American (AMR) AF: 0.903 AC: 13802 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3168 AN: 3472

East Asian (EAS) AF: 0.788 AC: 4078 AN: 5174

South Asian (SAS) AF: 0.945 AC: 4559 AN: 4826

European-Finnish (FIN) AF: 0.911 AC: 9665 AN: 10610

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59727 AN: 67996

Other (OTH) AF: 0.888 AC: 1877 AN: 2114

Alfa AF: 0.882 Hom.: 251429

Bravo AF: 0.894

Asia WGS AF: 0.866 AC: 3012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	11
DANN	Benign	0.61
PhyloP100		0.56
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: rs7225566; hg19: chr17-47798725;