rs2002030

chr8-11419033-T-Cchr8-11419033-T-G

Variant summary

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

The NR_026814.1(FAM167A-AS1):n.341-14887T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,110 control chromosomes in the GnomAD database, including 1,352 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 0.11 (1352 hom., cov: 32)
• Consequence: FAM167A-AS1 NR_026814.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM167A-AS1	NR_026814.1	n.341-14887T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM167A-AS1	ENST00000533578.4	n.341-14887T>C		intron_variant, non_coding_transcript_variant		2
FAM167A-AS1	ENST00000624614.1	n.474+14331T>C		intron_variant, non_coding_transcript_variant		1
FAM167A-AS1	ENST00000529305.5	n.413-14887T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17419 AN: 151992 Hom.: 1351 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0684

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.0649

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0745

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.115 AC: 17440 AN: 152110 Hom.: 1352 Cov.: 32 AF XY: 0.114 AC XY: 8506 AN XY: 74366

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.0682

Gnomad4 ASJ AF: 0.0931

Gnomad4 EAS AF: 0.0184

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.0649

Gnomad4 NFE AF: 0.0745

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0748 Hom.: 1105

Bravo AF: 0.117

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.5
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2002030; hg19: chr8-11276542;