rs7290139

Variant names:

• chr22-45322862-A-G
• rs7290139
• NM_017911.4:c.48-313A>G

Your query was ambiguous. Multiple possible variants found:

• chr22-45322862-A-G
• chr22-45322862-A-T

Variant summary

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

The NM_017911.4(FAM118A):​c.48-313A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 152,156 control chromosomes in the GnomAD database, including 17,560 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 0.43 (17560 hom., cov: 33)
• Consequence: FAM118A NM_017911.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 12 publications found

Genes affected

FAM118A (HGNC:1313): (family with sequence similarity 118 member A) Enables identical protein binding activity. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017911.4. 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
	FAM118A	NM_017911.4	MANE Select	c.48-313A>G		intron	N/A	NP_060381.2
	FAM118A	NM_001349916.2		c.90-313A>G		intron	N/A	NP_001336845.1
	FAM118A	NM_001349914.2		c.48-310A>G		intron	N/A	NP_001336843.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM118A	ENST00000441876.7	TSL:1 MANE Select	c.48-313A>G		intron	N/A	ENSP00000395892.2
	FAM118A	ENST00000216214.7	TSL:2	c.48-313A>G		intron	N/A	ENSP00000216214.3
	FAM118A	ENST00000405673.5	TSL:5	c.48-313A>G		intron	N/A	ENSP00000385231.1

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65710 AN: 152038 Hom.: 17560 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.432 AC: 65713 AN: 152156 Hom.: 17560 Cov.: 33 AF XY: 0.427 AC XY: 31733 AN XY: 74386

African (AFR) AF: 0.117 AC: 4852 AN: 41526

American (AMR) AF: 0.466 AC: 7122 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1755 AN: 3472

East Asian (EAS) AF: 0.330 AC: 1710 AN: 5176

South Asian (SAS) AF: 0.333 AC: 1609 AN: 4828

European-Finnish (FIN) AF: 0.556 AC: 5882 AN: 10572

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41230 AN: 67978

Other (OTH) AF: 0.445 AC: 940 AN: 2112

Alfa AF: 0.477 Hom.: 19890

Bravo AF: 0.416

Asia WGS AF: 0.275 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.085
DANN	Benign	0.36
PhyloP100		-1.4
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: rs7290139; hg19: chr22-45718743;