rs6467991

Variant names:

• chr7-84325421-A-C
• rs6467991
• ENST00000448879.5:c.-168-18129T>G

Your query was ambiguous. Multiple possible variants found:

• chr7-84325421-A-C
• chr7-84325421-A-G
• chr7-84325421-A-T

Variant summary

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

The ENST00000424555.5(SEMA3A):​c.-168-18129T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,860 control chromosomes in the GnomAD database, including 8,409 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 0.28 (8409 hom., cov: 31)
• Consequence: SEMA3A ENST00000424555.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560

Genes affected

SEMA3A (HGNC:10723): (semaphorin 3A) This gene is a member of the semaphorin family and encodes a protein with an Ig-like C2-type (immunoglobulin-like) domain, a PSI domain and a Sema domain. This secreted protein can function as either a chemorepulsive agent, inhibiting axonal outgrowth, or as a chemoattractive agent, stimulating the growth of apical dendrites. In both cases, the protein is vital for normal neuronal pattern development. Increased expression of this protein is associated with schizophrenia and is seen in a variety of human tumor cell lines. Also, aberrant release of this protein is associated with the progression of Alzheimer's disease. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEMA3A	XM_005250110.4	c.-168-18129T>G		intron_variant	Intron 2 of 19		XP_005250167.1
SEMA3A	XM_047419751.1	c.-258-18129T>G		intron_variant	Intron 2 of 20		XP_047275707.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEMA3A	ENST00000448879.5	c.-168-18129T>G		intron_variant	Intron 3 of 4	5		ENSP00000402093.1
SEMA3A	ENST00000424555.5	c.-168-18129T>G		intron_variant	Intron 2 of 3	4		ENSP00000404800.1
SEMA3A	ENST00000471474.5	n.373-18129T>G		intron_variant	Intron 2 of 3	5
SEMA3A	ENST00000490883.1	n.152-18129T>G		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42853 AN: 151740 Hom.: 8388 Cov.: 31

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.283 AC: 42924 AN: 151860 Hom.: 8409 Cov.: 31 AF XY: 0.282 AC XY: 20960 AN XY: 74206

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.264

Alfa AF: 0.171 Hom.: 3878

Bravo AF: 0.295

Asia WGS AF: 0.329 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.0
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6467991; hg19: chr7-83954737;