rs7789940

Variant names:

• chr7-76321913-A-G
• rs7789940
• NR_186616.1:n.2396A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-76321913-A-G
• chr7-76321913-A-T

Variant summary

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

The NR_186616.1(FPASL):​n.2396A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,010 control chromosomes in the GnomAD database, including 6,989 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 0.30 (6989 hom., cov: 31)
• Consequence: FPASL NR_186616.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 21 publications found

Genes affected

FPASL (HGNC:56688): (fibroblast proliferation associated lncRNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FPASL	NR_186616.1	n.2396A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FPASL	ENST00000803640.1	n.249-2983A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45515 AN: 151892 Hom.: 6983 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.300 AC: 45530 AN: 152010 Hom.: 6989 Cov.: 31 AF XY: 0.303 AC XY: 22525 AN XY: 74306

African (AFR) AF: 0.315 AC: 13073 AN: 41446

American (AMR) AF: 0.285 AC: 4355 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3470

East Asian (EAS) AF: 0.440 AC: 2273 AN: 5162

South Asian (SAS) AF: 0.209 AC: 1006 AN: 4818

European-Finnish (FIN) AF: 0.363 AC: 3830 AN: 10554

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19396 AN: 67986

Other (OTH) AF: 0.282 AC: 594 AN: 2108

Alfa AF: 0.291 Hom.: 23311

Bravo AF: 0.302

Asia WGS AF: 0.342 AC: 1194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.0
DANN	Benign	0.72
PhyloP100		0.073

Splicing

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

Other links and lift over

dbSNP: rs7789940; hg19: chr7-75951230;