rs2803662

chr9-41665682-G-Achr9-41665682-G-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000611780.4(FAM242F):n.224-7698C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.20 (1202 hom., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: FAM242F ENST00000611780.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205

Genes affected

FAM242F (HGNC:53876): (family with sequence similarity 242 member F)

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=0.391).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM242F	ENST00000611780.4	n.224-7698C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 16329 AN: 79810 Hom.: 1205 Cov.: 20 FAILED QC

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.197

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.204 AC: 16328 AN: 79910 Hom.: 1202 Cov.: 20 AF XY: 0.194 AC XY: 7561 AN XY: 38886

Gnomad4 AFR AF: 0.0793

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.196

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Cadd	Benign	0.39
Dann	Benign	0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2803662; hg19: -;