rs739983

Positions:

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

Variant summary

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

The NR_135301.1(SEMA3F-AS1):​n.353-4010C>T 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 0.531 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 NR_135301.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SEMA3F-AS1	NR_135301.1	n.353-4010C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEMA3F-AS1	ENST00000437204.1	n.353-4010C>T		intron_variant, non_coding_transcript_variant		2
SEMA3F-AS1	ENST00000425674.1	n.287+15156C>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.526

Alfa AF: 0.607 Hom.: 42337

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs739983; hg19: chr3-50178011;