rs10079121

Variant names:

• chr5-9228537-C-A
• rs10079121
• NM_003966.3:c.334-1570G>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.334-1570G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,154 control chromosomes in the GnomAD database, including 3,958 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 0.22 (3958 hom., cov: 33)
• Consequence: SEMA5A NM_003966.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.301 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEMA5A	NM_003966.3	MANE Select	c.334-1570G>T		intron	N/A	NP_003957.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEMA5A	ENST00000382496.10	TSL:1 MANE Select	c.334-1570G>T		intron	N/A	ENSP00000371936.5
	SEMA5A	ENST00000652226.1		c.334-1570G>T		intron	N/A	ENSP00000499013.1
	SEMA5A	ENST00000513968.4	TSL:5	c.334-1570G>T		intron	N/A	ENSP00000421961.1

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33037 AN: 152036 Hom.: 3949 Cov.: 33

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.217 AC: 33089 AN: 152154 Hom.: 3958 Cov.: 33 AF XY: 0.220 AC XY: 16382 AN XY: 74376

African (AFR) AF: 0.306 AC: 12684 AN: 41492

American (AMR) AF: 0.283 AC: 4322 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 828 AN: 3464

East Asian (EAS) AF: 0.296 AC: 1528 AN: 5164

South Asian (SAS) AF: 0.125 AC: 602 AN: 4820

European-Finnish (FIN) AF: 0.202 AC: 2140 AN: 10592

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.150 AC: 10225 AN: 68016

Other (OTH) AF: 0.230 AC: 486 AN: 2110

Alfa AF: 0.191 Hom.: 2100

Bravo AF: 0.233

Asia WGS AF: 0.235 AC: 815 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	0.78
DANN	Benign	0.64
PhyloP100		-0.35
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: rs10079121; hg19: chr5-9228649;