17-49712503-G-C

Variant names:

• chr17-49712503-G-C
• rs8064701
• NM_030802.4:c.1062-948C>G

Variant summary

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

The NM_030802.4(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 NM_030802.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 2 publications found

Genes affected

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

ENSG00000250751 (HGNC:):

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 = 0.921 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.1062-948C>G		intron	N/A	NP_110429.1
	FAM117A	NM_001411126.1		c.246-948C>G		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.1062-948C>G		intron	N/A	ENSP00000240364.2
	FAM117A	ENST00000513602.5	TSL:2	c.246-948C>G		intron	N/A	ENSP00000465808.1
	FAM117A	ENST00000503573.5	TSL:5	n.*398-948C>G		intron	N/A	ENSP00000467070.1

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

African (AFR) AF: 0.886 AC: 36777 AN: 41510

American (AMR) AF: 0.899 AC: 13745 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3167 AN: 3472

East Asian (EAS) AF: 0.789 AC: 4074 AN: 5166

South Asian (SAS) AF: 0.944 AC: 4549 AN: 4818

European-Finnish (FIN) AF: 0.911 AC: 9663 AN: 10608

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

European-Non Finnish (NFE) AF: 0.878 AC: 59739 AN: 68016

Other (OTH) AF: 0.881 AC: 1857 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.40
DANN	Benign	0.59
PhyloP100		-1.9
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: rs8064701; hg19: chr17-47789865;