rs7290139

chr22-45322862-A-Gchr22-45322862-A-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM118A	NM_017911.4	c.48-313A>G		intron_variant		ENST00000441876.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM118A	ENST00000441876.7	c.48-313A>G		intron_variant		1	NM_017911.4	P1

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

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.445

Alfa AF: 0.528 Hom.: 12000

Bravo AF: 0.416

Asia WGS AF: 0.275 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.085
Dann	Benign	0.36

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: rs7290139; hg19: chr22-45718743;