rs9967638

Positions:

• chr19-53303399-C-G

Variant summary

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

The ENST00000596881.1(ENSG00000290987):​n.254-292G>C variant causes a intron, non coding transcript 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 0.24 (308 hom., cov: 0)
• Consequence: ENST00000596881.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885

Genes affected

(HGNC:):

FAM90A28P (HGNC:43747): (family with sequence similarity 90 member A28, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987270	XR_001753995.1	n.188-292G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000596881.1	n.254-292G>C		intron_variant, non_coding_transcript_variant		5
FAM90A28P	ENST00000597191.2	n.73-292G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.240 AC: 8103 AN: 33772 Hom.: 307 Cov.: 0

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.0930

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.262

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.240 AC: 8114 AN: 33818 Hom.: 308 Cov.: 0 AF XY: 0.237 AC XY: 3881 AN XY: 16398

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.262

Alfa AF: 0.133 Hom.: 26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.44
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9967638; hg19: chr19-53806652;