ENST00000624614.1:n.474+9953G>A

Variant names:

• chr8-11414655-G-A
• rs7836059
• ENST00000624614.1:n.474+9953G>A

Variant summary

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

The ENST00000624614.1(FAM167A-AS1):​n.474+9953G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,844 control chromosomes in the GnomAD database, including 20,118 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 0.49 (20118 hom., cov: 30)
• Consequence: FAM167A-AS1 ENST00000624614.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 20 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000624614.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM167A-AS1	NR_026814.1		n.340+13490G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM167A-AS1	ENST00000624614.1	TSL:1	n.474+9953G>A		intron	N/A
	FAM167A-AS1	ENST00000529305.5	TSL:2	n.412+13490G>A		intron	N/A
	FAM167A-AS1	ENST00000533578.5	TSL:2	n.340+13490G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74882 AN: 151726 Hom.: 20093 Cov.: 30

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.0602

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.494 AC: 74953 AN: 151844 Hom.: 20118 Cov.: 30 AF XY: 0.482 AC XY: 35776 AN XY: 74184

African (AFR) AF: 0.669 AC: 27657 AN: 41370

American (AMR) AF: 0.327 AC: 4985 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2226 AN: 3464

East Asian (EAS) AF: 0.0597 AC: 309 AN: 5174

South Asian (SAS) AF: 0.456 AC: 2193 AN: 4806

European-Finnish (FIN) AF: 0.353 AC: 3711 AN: 10504

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32333 AN: 67968

Other (OTH) AF: 0.461 AC: 970 AN: 2106

Alfa AF: 0.483 Hom.: 30274

Bravo AF: 0.494

Asia WGS AF: 0.320 AC: 1117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.23
PhyloP100		-0.22
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: rs7836059; hg19: chr8-11272164;