8-11382253-A-T

Position:

• chr8-11382253-A-T

Variant summary

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

The ENST00000533578.4(FAM167A-AS1):​n.52-1560A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 152,022 control chromosomes in the GnomAD database, including 26,030 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 0.54 (26030 hom., cov: 32)
• Consequence: FAM167A-AS1 ENST00000533578.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

Genes affected

FAM167A-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM167A-AS1	NR_026814.1	n.52-1560A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM167A-AS1	ENST00000533578.4	n.52-1560A>T		intron_variant		2
FAM167A-AS1	ENST00000655944.1	n.153-1560A>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82025 AN: 151904 Hom.: 25977 Cov.: 32

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.0222

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.540 AC: 82123 AN: 152022 Hom.: 26030 Cov.: 32 AF XY: 0.525 AC XY: 39041 AN XY: 74294

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.0222

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.512

Alfa AF: 0.393 Hom.: 1144

Bravo AF: 0.553

Asia WGS AF: 0.258 AC: 899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2736306; hg19: chr8-11239762;