rs9967638

Variant names:

• chr19-53303399-C-G
• rs9967638
• ENST00000596881.2:n.254-292G>C

Variant summary

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

The XR_001753995.1(LOC107987270):​n.188-292G>C 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 0.24 (308 hom., cov: 0)
• Consequence: LOC107987270 XR_001753995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885
• Publications: 1 publications found

Genes affected

ENSG00000290987 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000596881.2. 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
	ENSG00000290987	ENST00000596881.2	TSL:5	n.254-292G>C		intron	N/A
	FAM90A28P	ENST00000597191.2	TSL:6	n.73-292G>C		intron	N/A

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

African (AFR) AF: 0.343 AC: 4009 AN: 11684

American (AMR) AF: 0.163 AC: 613 AN: 3770

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 143 AN: 604

East Asian (EAS) AF: 0.264 AC: 325 AN: 1232

South Asian (SAS) AF: 0.195 AC: 190 AN: 974

European-Finnish (FIN) AF: 0.164 AC: 329 AN: 2006

Middle Eastern (MID) AF: 0.186 AC: 13 AN: 70

European-Non Finnish (NFE) AF: 0.183 AC: 2365 AN: 12938

Other (OTH) AF: 0.262 AC: 119 AN: 454

Alfa AF: 0.133 Hom.: 26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.44
DANN	Benign	0.21
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs9967638; hg19: chr19-53806652;