8-11382253-A-T

Variant names:

• chr8-11382253-A-T
• rs2736306
• ENST00000533578.5:n.52-1560A>T

Variant summary

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

The ENST00000533578.5(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 ENST00000533578.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 13 publications found

Genes affected

FAM167A-AS1 (HGNC:15548): (FAM167A antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FAM167A-AS1	NR_026814.1	n.52-1560A>T		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM167A-AS1	ENST00000533578.5	n.52-1560A>T		intron_variant	Intron 1 of 6	2
FAM167A-AS1	ENST00000655944.1	n.153-1560A>T		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.868 AC: 36014 AN: 41490

American (AMR) AF: 0.379 AC: 5790 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2119 AN: 3468

East Asian (EAS) AF: 0.0222 AC: 115 AN: 5178

South Asian (SAS) AF: 0.340 AC: 1635 AN: 4810

European-Finnish (FIN) AF: 0.350 AC: 3689 AN: 10538

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31225 AN: 67950

Other (OTH) AF: 0.512 AC: 1080 AN: 2110

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
PhyloP100		-0.16
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2736306; hg19: chr8-11239762;