rs3777306

Variant names:

• chr5-9295569-C-A
• rs3777306
• NM_003966.3:c.270+22803G>T

Your query was ambiguous. Multiple possible variants found:

• chr5-9295569-C-A
• chr5-9295569-C-T

Variant summary

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

The NM_003966.3(SEMA5A):​c.270+22803G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,032 control chromosomes in the GnomAD database, including 1,403 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 0.13 (1403 hom., cov: 32)
• Consequence: SEMA5A NM_003966.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.343
• Publications: 2 publications found

Genes affected

SEMA5A (HGNC:10736): (semaphorin 5A) This gene belongs to the semaphorin gene family that encodes membrane proteins containing a semaphorin domain and several thrombospondin type-1 repeats. Members of this family are involved in axonal guidance during neural development. This gene has been implicated as an autism susceptibility gene.[provided by RefSeq, Jan 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003966.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEMA5A	NM_003966.3	MANE Select	c.270+22803G>T		intron	N/A	NP_003957.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEMA5A	ENST00000382496.10	TSL:1 MANE Select	c.270+22803G>T		intron	N/A	ENSP00000371936.5
	SEMA5A	ENST00000652226.1		c.270+22803G>T		intron	N/A	ENSP00000499013.1
	SEMA5A	ENST00000897596.1		c.270+22803G>T		intron	N/A	ENSP00000567655.1

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20088 AN: 151914 Hom.: 1401 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.0722

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.132 AC: 20115 AN: 152032 Hom.: 1403 Cov.: 32 AF XY: 0.134 AC XY: 9931 AN XY: 74320

African (AFR) AF: 0.143 AC: 5918 AN: 41470

American (AMR) AF: 0.134 AC: 2045 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 433 AN: 3466

East Asian (EAS) AF: 0.0726 AC: 375 AN: 5168

South Asian (SAS) AF: 0.193 AC: 930 AN: 4814

European-Finnish (FIN) AF: 0.117 AC: 1241 AN: 10576

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8569 AN: 67950

Other (OTH) AF: 0.151 AC: 320 AN: 2114

Alfa AF: 0.125 Hom.: 5225

Bravo AF: 0.131

Asia WGS AF: 0.136 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.46
PhyloP100		0.34
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3777306; hg19: chr5-9295681;