chr1-107990240-T-C

Variant names:

• chr1-107990240-T-C
• rs1219776
• ENST00000438318.1:n.63-3265T>C

Variant summary

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

The ENST00000438318.1(VAV3-AS1):​n.63-3265T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.949 in 152,252 control chromosomes in the GnomAD database, including 69,026 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 0.95 (69026 hom., cov: 31)
• Consequence: VAV3-AS1 ENST00000438318.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.789
• Publications: 1 publications found

Genes affected

VAV3-AS1 (HGNC:40608): (VAV3 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438318.1. 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
	VAV3-AS1	NR_046653.1		n.63-3265T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VAV3-AS1	ENST00000438318.1	TSL:2	n.63-3265T>C		intron	N/A
	VAV3-AS1	ENST00000715653.1		n.138+25736T>C		intron	N/A
	VAV3-AS1	ENST00000820014.1		n.134+25736T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.950 AC: 144475 AN: 152134 Hom.: 68997 Cov.: 31

Gnomad AFR AF: 0.837

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.977

Gnomad ASJ AF: 0.990

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.959

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

GnomAD4 genome AF: 0.949 AC: 144559 AN: 152252 Hom.: 69026 Cov.: 31 AF XY: 0.951 AC XY: 70819 AN XY: 74430

African (AFR) AF: 0.836 AC: 34724 AN: 41530

American (AMR) AF: 0.977 AC: 14933 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.990 AC: 3438 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5162 AN: 5162

South Asian (SAS) AF: 0.998 AC: 4820 AN: 4828

European-Finnish (FIN) AF: 0.999 AC: 10610 AN: 10616

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.994 AC: 67652 AN: 68036

Other (OTH) AF: 0.959 AC: 2026 AN: 2112

Alfa AF: 0.947 Hom.: 31733

Bravo AF: 0.942

Asia WGS AF: 0.986 AC: 3430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.5
DANN	Benign	0.63
PhyloP100		0.79

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1219776;

hg19: chr1-108532862;