rs7225566

chr17-49721363-A-Gchr17-49721363-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM117A	NM_030802.4	c.463-927T>C		intron_variant		ENST00000240364.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM117A	ENST00000240364.7	c.463-927T>C		intron_variant		1	NM_030802.4	P1

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

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.903

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.788

Gnomad4 SAS AF: 0.945

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.888

Alfa AF: 0.882 Hom.: 117995

Bravo AF: 0.894

Asia WGS AF: 0.866 AC: 3012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	11
Dann	Benign	0.61

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: rs7225566; hg19: chr17-47798725;