9-41665682-G-A

Variant names:

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

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>T 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 0.20 (1202 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=0.391).

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>T		intron_variant	Intron 2 of 2	5
ENSG00000275297	ENST00000748930.1	n.191+21439G>A		intron_variant	Intron 1 of 3
ENSG00000275297	ENST00000748931.1	n.257+21439G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.205 AC: 16329 AN: 79810 Hom.: 1205 Cov.: 20

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0793 AC: 2249 AN: 28344

American (AMR) AF: 0.171 AC: 1287 AN: 7538

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 367 AN: 1474

East Asian (EAS) AF: 0.216 AC: 450 AN: 2088

South Asian (SAS) AF: 0.138 AC: 363 AN: 2630

European-Finnish (FIN) AF: 0.347 AC: 1786 AN: 5140

Middle Eastern (MID) AF: 0.333 AC: 54 AN: 162

European-Non Finnish (NFE) AF: 0.304 AC: 9414 AN: 31000

Other (OTH) AF: 0.196 AC: 218 AN: 1114

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.39
DANN	Benign	0.26
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: -;