rs2064068

chr22-45340604-C-T

Variant summary

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

The NM_017911.4(FAM118A):c.*199C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 613,240 control chromosomes in the GnomAD database, including 73,072 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 0.40 (14619 hom., cov: 31)
  • Exomes 𝑓: 0.49 (58453 hom.)
• Consequence: FAM118A NM_017911.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM118A	NM_017911.4	c.*199C>T		3_prime_UTR_variant	9/9	ENST00000441876.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM118A	ENST00000441876.7	c.*199C>T		3_prime_UTR_variant	9/9	1	NM_017911.4	P1

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60250 AN: 151828 Hom.: 14619 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.414

GnomAD4 exome AF: 0.492 AC: 227026 AN: 461294 Hom.: 58453 Cov.: 5 AF XY: 0.490 AC XY: 119666 AN XY: 244182

Gnomad4 AFR exome AF: 0.112

Gnomad4 AMR exome AF: 0.474

Gnomad4 ASJ exome AF: 0.495

Gnomad4 EAS exome AF: 0.394

Gnomad4 SAS exome AF: 0.361

Gnomad4 FIN exome AF: 0.486

Gnomad4 NFE exome AF: 0.546

Gnomad4 OTH exome AF: 0.461

GnomAD4 genome AF: 0.397 AC: 60256 AN: 151946 Hom.: 14619 Cov.: 31 AF XY: 0.391 AC XY: 29055 AN XY: 74280

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.408

Alfa AF: 0.514 Hom.: 20075

Bravo AF: 0.385

Asia WGS AF: 0.266 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	1.2
Dann	Benign	0.66

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: rs2064068; hg19: chr22-45736485; COSMIC: COSV53416966; COSMIC: COSV53416966;