rs8064701

Positions:

• chr17-49712503-G-C

Variant summary

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

The ENST00000240364.7(FAM117A):​c.1062-948C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.885 in 152,192 control chromosomes in the GnomAD database, including 59,665 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 0.89 (59665 hom., cov: 31)
• Consequence: FAM117A ENST00000240364.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92

Genes affected

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

(HGNC:):

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 = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM117A	NM_030802.4	c.1062-948C>G		intron_variant		ENST00000240364.7	NP_110429.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM117A	ENST00000240364.7	c.1062-948C>G		intron_variant		1	NM_030802.4	ENSP00000240364	P1
	ENST00000512720.1	n.142+4028G>C		intron_variant, non_coding_transcript_variant		3
FAM117A	ENST00000513602.5	c.246-948C>G		intron_variant		2		ENSP00000465808
FAM117A	ENST00000503573.5	c.*398-948C>G		intron_variant, NMD_transcript_variant		5		ENSP00000467070

Frequencies

GnomAD3 genomes AF: 0.885 AC: 134580 AN: 152074 Hom.: 59607 Cov.: 31

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.943

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.885 AC: 134695 AN: 152192 Hom.: 59665 Cov.: 31 AF XY: 0.887 AC XY: 65970 AN XY: 74416

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.899

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.944

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.881

Alfa AF: 0.882 Hom.: 7351

Bravo AF: 0.882

Asia WGS AF: 0.867 AC: 3014 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	0.40
DANN	Benign	0.59

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: rs8064701; hg19: chr17-47789865;