rs329007

Variant names:

• chr18-9522608-G-A
• rs329007
• NM_006788.4:c.1053+99G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-9522608-G-A
• chr18-9522608-G-C

Variant summary

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

The NM_006788.4(RALBP1):​c.1053+99G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 966,870 control chromosomes in the GnomAD database, including 280,615 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 0.78 (47211 hom., cov: 33)
  • Exomes 𝑓: 0.75 (233404 hom.)
• Consequence: RALBP1 NM_006788.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 15 publications found

Genes affected

RALBP1 (HGNC:9841): (ralA binding protein 1) RALBP1 plays a role in receptor-mediated endocytosis and is a downstream effector of the small GTP-binding protein RAL (see RALA; MIM 179550). Small G proteins, such as RAL, have GDP-bound inactive and GTP-bound active forms, which shift from the inactive to the active state through the action of RALGDS (MIM 601619), which in turn is activated by RAS (see HRAS; MIM 190020) (summary by Feig, 2003 [PubMed 12888294]).[supplied by OMIM, Nov 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006788.4. 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
	RALBP1	NM_006788.4	MANE Select	c.1053+99G>A		intron	N/A	NP_006779.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RALBP1	ENST00000383432.8	TSL:1 MANE Select	c.1053+99G>A		intron	N/A	ENSP00000372924.3
	RALBP1	ENST00000019317.8	TSL:1	c.1053+99G>A		intron	N/A	ENSP00000019317.4

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119331 AN: 152132 Hom.: 47168 Cov.: 33

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.781

GnomAD4 exome AF: 0.754 AC: 613927 AN: 814618 Hom.: 233404 AF XY: 0.748 AC XY: 310059 AN XY: 414336

African (AFR) AF: 0.848 AC: 16311 AN: 19242

American (AMR) AF: 0.721 AC: 17412 AN: 24134

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 13116 AN: 16580

East Asian (EAS) AF: 0.578 AC: 19695 AN: 34050

South Asian (SAS) AF: 0.612 AC: 33871 AN: 55358

European-Finnish (FIN) AF: 0.857 AC: 31351 AN: 36598

Middle Eastern (MID) AF: 0.817 AC: 3542 AN: 4336

European-Non Finnish (NFE) AF: 0.767 AC: 449432 AN: 585970

Other (OTH) AF: 0.761 AC: 29197 AN: 38350

GnomAD4 genome AF: 0.784 AC: 119434 AN: 152252 Hom.: 47211 Cov.: 33 AF XY: 0.782 AC XY: 58226 AN XY: 74432

African (AFR) AF: 0.841 AC: 34954 AN: 41554

American (AMR) AF: 0.744 AC: 11380 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2764 AN: 3472

East Asian (EAS) AF: 0.584 AC: 3022 AN: 5176

South Asian (SAS) AF: 0.606 AC: 2928 AN: 4828

European-Finnish (FIN) AF: 0.866 AC: 9185 AN: 10608

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52572 AN: 67996

Other (OTH) AF: 0.776 AC: 1641 AN: 2114

Alfa AF: 0.769 Hom.: 142422

Bravo AF: 0.780

Asia WGS AF: 0.566 AC: 1970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.75
DANN	Benign	0.62
PhyloP100		-0.17
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: rs329007; hg19: chr18-9522606;