rs7778955

chr7-39700888-A-Gchr7-39700888-A-T

Variant summary

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

The NM_005402.4(RALA):c.498+4029A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,134 control chromosomes in the GnomAD database, including 8,232 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 0.31 (8232 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: RALA NM_005402.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

Genes affected

RALA (HGNC:9839): (RAS like proto-oncogene A) The product of this gene belongs to the small GTPase superfamily, Ras family of proteins. GTP-binding proteins mediate the transmembrane signaling initiated by the occupancy of certain cell surface receptors. This gene encodes a low molecular mass ras-like GTP-binding protein that shares about 50% similarity with other ras proteins. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RALA	NM_005402.4	c.498+4029A>G		intron_variant		ENST00000005257.7
RALA	XM_047420681.1	c.498+4029A>G		intron_variant
RALA	XM_047420682.1	c.498+4029A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RALA	ENST00000005257.7	c.498+4029A>G		intron_variant		1	NM_005402.4	P1
	ENST00000435766.1	n.318-134T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47625 AN: 152014 Hom.: 8235 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0340

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.280

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.313 AC: 47634 AN: 152132 Hom.: 8232 Cov.: 32 AF XY: 0.309 AC XY: 22975 AN XY: 74376

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.0338

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.277

Alfa AF: 0.364 Hom.: 21366

Bravo AF: 0.298

Asia WGS AF: 0.206 AC: 720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.9
Dann	Benign	0.58

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

Publications

LitVar

Other links and lift over

dbSNP: rs7778955; hg19: chr7-39740487;