9-41665682-G-C

Variant names:

• chr9-41665682-G-C
• rs2803662
• ENST00000611780.4:n.224-7698C>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000611780.4(FAM242F):​n.224-7698C>G variant causes a intron 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 0.0 (0 hom., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: FAM242F ENST00000611780.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 1 publications found

Genes affected

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

ENSG00000275297 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=0.331).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM242F	ENST00000611780.4	n.224-7698C>G		intron_variant	Intron 2 of 2	5
ENSG00000275297	ENST00000748930.1	n.191+21439G>C		intron_variant	Intron 1 of 3
ENSG00000275297	ENST00000748931.1	n.257+21439G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 100800 Hom.: 0 Cov.: 20

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 100800 Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0 AN XY: 48706

African (AFR) AF: 0.00 AC: 0 AN: 32616

American (AMR) AF: 0.00 AC: 0 AN: 9142

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1948

East Asian (EAS) AF: 0.00 AC: 0 AN: 2494

South Asian (SAS) AF: 0.00 AC: 0 AN: 3134

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6834

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 226

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 42460

Other (OTH) AF: 0.00 AC: 0 AN: 1362

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.33
DANN	Benign	0.51
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2803662; hg19: -;