rs2803662

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-41665682-G-A
• chr9-41665682-G-C

Variant summary

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

The ENST00000748930.1(ENSG00000275297):​n.191+21439G>A 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: ENSG00000275297 ENST00000748930.1 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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748930.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM242F	ENST00000611780.4	TSL:5	n.224-7698C>T		intron	N/A
	ENSG00000275297	ENST00000748930.1		n.191+21439G>A		intron	N/A
	ENSG00000275297	ENST00000748931.1		n.257+21439G>A		intron	N/A

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), 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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2803662;