rs6519442

Variant names:

• chr22-23471071-T-G
• rs6519442
• ENST00000320372.9:n.465A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000320372.9(FAM230I):​n.465A>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 ENST00000320372.9 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FAM230I	NR_110539.2	n.465A>C		non_coding_transcript_exon_variant	Exon 7 of 12
FAM230I	NR_165488.1	n.434A>C		non_coding_transcript_exon_variant	Exon 6 of 10
FAM230I	NR_165489.1	n.465A>C		non_coding_transcript_exon_variant	Exon 7 of 11
FAM230I	NR_165490.1	n.465A>C		non_coding_transcript_exon_variant	Exon 7 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM230I	ENST00000320372.9	n.465A>C		non_coding_transcript_exon_variant	Exon 7 of 12	2
FAM230I	ENST00000785831.1	n.758A>C		non_coding_transcript_exon_variant	Exon 8 of 13
FAM230I	ENST00000785832.1	n.442A>C		non_coding_transcript_exon_variant	Exon 7 of 10

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

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.250 AC: 1 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.294 AC: 188 AN: 640

Middle Eastern (MID) AF: 0.250 AC: 1 AN: 4

European-Non Finnish (NFE) AF: 0.287 AC: 47 AN: 164

Other (OTH) AF: 0.250 AC: 38 AN: 152

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

African (AFR) AF: 0.205 AC: 8489 AN: 41502

American (AMR) AF: 0.219 AC: 3358 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1127 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5180

South Asian (SAS) AF: 0.161 AC: 777 AN: 4832

European-Finnish (FIN) AF: 0.253 AC: 2677 AN: 10582

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20590 AN: 67992

Other (OTH) AF: 0.261 AC: 552 AN: 2112

Alfa AF: 0.282 Hom.: 19142

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
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs6519442; hg19: chr22-23813258;