rs2002030

Variant names:

• chr8-11419033-T-C
• rs2002030
• ENST00000624614.1:n.474+14331T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-11419033-T-C
• chr8-11419033-T-G

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+14331T>C variant causes a intron 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 ENST00000624614.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 14 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=-0.91).
• 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 rank	MANE	Protein	UniProt
FAM167A-AS1	NR_026814.1	n.341-14887T>C		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM167A-AS1	ENST00000624614.1	n.474+14331T>C		intron_variant	Intron 3 of 6	1
FAM167A-AS1	ENST00000529305.5	n.413-14887T>C		intron_variant	Intron 2 of 3	2
FAM167A-AS1	ENST00000533578.5	n.341-14887T>C		intron_variant	Intron 3 of 6	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

African (AFR) AF: 0.220 AC: 9125 AN: 41454

American (AMR) AF: 0.0682 AC: 1043 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0931 AC: 323 AN: 3470

East Asian (EAS) AF: 0.0184 AC: 95 AN: 5168

South Asian (SAS) AF: 0.177 AC: 850 AN: 4810

European-Finnish (FIN) AF: 0.0649 AC: 687 AN: 10582

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0745 AC: 5070 AN: 68016

Other (OTH) AF: 0.100 AC: 212 AN: 2112

Alfa AF: 0.0831 Hom.: 2827

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
PhyloP100		-0.15
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: rs2002030; hg19: chr8-11276542;