rs7997328

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000820.4(GAS6):​c.255+7126T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 152,004 control chromosomes in the GnomAD database, including 17,161 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 0.44 ( 17161 hom., cov: 32)

Consequence

GAS6
NM_000820.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.873
Variant links:
Genes affected
GAS6 (HGNC:4168): (growth arrest specific 6) This gene encodes a gamma-carboxyglutamic acid (Gla)-containing protein thought to be involved in the stimulation of cell proliferation. This gene is frequently overexpressed in many cancers and has been implicated as an adverse prognostic marker. Elevated protein levels are additionally associated with a variety of disease states, including venous thromboembolic disease, systemic lupus erythematosus, chronic renal failure, and preeclampsia. [provided by RefSeq, Aug 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GAS6NM_000820.4 linkuse as main transcriptc.255+7126T>C intron_variant ENST00000327773.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GAS6ENST00000327773.7 linkuse as main transcriptc.255+7126T>C intron_variant 1 NM_000820.4 P1Q14393-2
GAS6ENST00000476291.1 linkuse as main transcriptn.350+7126T>C intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.436
AC:
66159
AN:
151886
Hom.:
17126
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.724
Gnomad AMI
AF:
0.316
Gnomad AMR
AF:
0.404
Gnomad ASJ
AF:
0.261
Gnomad EAS
AF:
0.469
Gnomad SAS
AF:
0.566
Gnomad FIN
AF:
0.312
Gnomad MID
AF:
0.440
Gnomad NFE
AF:
0.286
Gnomad OTH
AF:
0.417
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.436
AC:
66255
AN:
152004
Hom.:
17161
Cov.:
32
AF XY:
0.440
AC XY:
32690
AN XY:
74292
show subpopulations
Gnomad4 AFR
AF:
0.724
Gnomad4 AMR
AF:
0.404
Gnomad4 ASJ
AF:
0.261
Gnomad4 EAS
AF:
0.469
Gnomad4 SAS
AF:
0.566
Gnomad4 FIN
AF:
0.312
Gnomad4 NFE
AF:
0.286
Gnomad4 OTH
AF:
0.421
Alfa
AF:
0.341
Hom.:
4044
Bravo
AF:
0.448
Asia WGS
AF:
0.568
AC:
1976
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.58
DANN
Benign
0.33
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7997328; hg19: chr13-114559422; API