rs6519442

Positions:

• chr22-23471071-T-G

Variant summary

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

The NR_165488.1(FAM230I):​n.434A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 153,142 control chromosomes in the GnomAD database, including 5,183 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 0.25 (5143 hom., cov: 33)
  • Exomes 𝑓: 0.28 (40 hom.)
• Consequence: FAM230I NR_165488.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274

Genes affected

FAM230I (HGNC:52446): (family with sequence similarity 230 member I)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM230I	NR_165488.1	n.434A>C		non_coding_transcript_exon_variant	6/10
FAM230I	NR_110539.2	n.465A>C		non_coding_transcript_exon_variant	7/12
FAM230I	NR_165489.1	n.465A>C		non_coding_transcript_exon_variant	7/11
FAM230I	NR_165490.1	n.465A>C		non_coding_transcript_exon_variant	7/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM230I	ENST00000320372.9	n.465A>C		non_coding_transcript_exon_variant	7/12	2

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37990 AN: 152056 Hom.: 5147 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.264

GnomAD4 exome AF: 0.284 AC: 275 AN: 968 Hom.: 40 Cov.: 0 AF XY: 0.272 AC XY: 142 AN XY: 522

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.250

Gnomad4 FIN exome AF: 0.294

Gnomad4 NFE exome AF: 0.287

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.250 AC: 37990 AN: 152174 Hom.: 5143 Cov.: 33 AF XY: 0.244 AC XY: 18138 AN XY: 74378

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.261

Alfa AF: 0.292 Hom.: 13205

Bravo AF: 0.248

Asia WGS AF: 0.0840 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	0.87
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6519442; hg19: chr22-23813258;