rs739983

Variant names:

• chr3-50140578-G-A
• rs739983
• ENST00000425674.1:n.287+15156C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-50140578-G-A
• chr3-50140578-G-C

Variant summary

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

The ENST00000425674.1(SEMA3F-AS1):​n.287+15156C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,962 control chromosomes in the GnomAD database, including 22,596 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 0.53 (22596 hom., cov: 31)
• Consequence: SEMA3F-AS1 ENST00000425674.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285
• Publications: 11 publications found

Genes affected

SEMA3F-AS1 (HGNC:40518): (SEMA3F antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEMA3F-AS1	NR_135301.1	n.353-4010C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEMA3F-AS1	ENST00000425674.1	n.287+15156C>T		intron_variant	Intron 1 of 1	4
SEMA3F-AS1	ENST00000437204.1	n.353-4010C>T		intron_variant	Intron 1 of 3	2
SEMA3F-AS1	ENST00000844078.1	n.257-4010C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80596 AN: 151844 Hom.: 22587 Cov.: 31

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.531 AC: 80622 AN: 151962 Hom.: 22596 Cov.: 31 AF XY: 0.524 AC XY: 38885 AN XY: 74268

African (AFR) AF: 0.431 AC: 17865 AN: 41438

American (AMR) AF: 0.423 AC: 6462 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1893 AN: 3472

East Asian (EAS) AF: 0.148 AC: 768 AN: 5178

South Asian (SAS) AF: 0.506 AC: 2436 AN: 4812

European-Finnish (FIN) AF: 0.589 AC: 6219 AN: 10554

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43256 AN: 67926

Other (OTH) AF: 0.526 AC: 1112 AN: 2114

Alfa AF: 0.587 Hom.: 74556

Bravo AF: 0.509

Asia WGS AF: 0.376 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.2
DANN	Benign	0.79
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs739983; hg19: chr3-50178011;